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WO2007067814A2 - Ciblage de proteines gli dans un cancer humain par de petites molecules - Google Patents

Ciblage de proteines gli dans un cancer humain par de petites molecules Download PDF

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Publication number
WO2007067814A2
WO2007067814A2 PCT/US2006/047231 US2006047231W WO2007067814A2 WO 2007067814 A2 WO2007067814 A2 WO 2007067814A2 US 2006047231 W US2006047231 W US 2006047231W WO 2007067814 A2 WO2007067814 A2 WO 2007067814A2
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Prior art keywords
small molecule
gli
cell
protein
cancer
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WO2007067814A3 (fr
Inventor
Biao He
Naoaki Fujii
Liang You
Zhidong Xu
David M. Jablons
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University of California Berkeley
University of California San Diego UCSD
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University of California Berkeley
University of California San Diego UCSD
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Priority to AU2006321729A priority Critical patent/AU2006321729A1/en
Priority to JP2008544584A priority patent/JP5149807B2/ja
Priority to EP06845208A priority patent/EP1968577B1/fr
Priority to CA2632813A priority patent/CA2632813C/fr
Publication of WO2007067814A2 publication Critical patent/WO2007067814A2/fr
Publication of WO2007067814A3 publication Critical patent/WO2007067814A3/fr
Priority to IL191999A priority patent/IL191999A0/en
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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07D—HETEROCYCLIC COMPOUNDS
    • C07D231/00—Heterocyclic compounds containing 1,2-diazole or hydrogenated 1,2-diazole rings
    • C07D231/02—Heterocyclic compounds containing 1,2-diazole or hydrogenated 1,2-diazole rings not condensed with other rings
    • C07D231/06—Heterocyclic compounds containing 1,2-diazole or hydrogenated 1,2-diazole rings not condensed with other rings having one double bond between ring members or between a ring member and a non-ring member
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P43/00—Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00

Definitions

  • the present invention relates generally to compositions and methods of inhibiting tumorigenesis, tumor growth and tumor survival.
  • the compositions comprise small molecule compounds inhibiting Hedgehog and GLI signaling pathways.
  • Hedgehog (Shh or Hh), WNT, FGF and BMP signaling pathways network together during embryogenesis, tissue regeneration, and carcinogenesis.
  • Aberrant activation of Hh signaling pathways leads to pathological consequences in a variety of human rumors, such as gastric cancer and pancreatic cancer.
  • Hedgehogs are secreted glycoproteins that initiate Hh signal transduction by binding to a transmembrane protein complex comprising PATCHEDl (ptchl) and SMOOTHENED (smo) and eliciting a cascade of cytoplasmic signal transduction events, including the inhibition of a protein kinase A that leads to the transcription of the GLI zinc-finger transcription factors.
  • the GLI family of zinc-finger transcription factors then translate the extra-cellular Hh-stimulus into defined transcriptional programs in a context- dependent and cell-type specific manner (Ruiz I Altaba et ah, 2002, Nat. Rev. Cancer 2:361 - 72).
  • GLI GLI proteins
  • GLI2 GLI2
  • GLI3 GLI2
  • Ci Drosophila Cubitus interruptus
  • Caenorhabditis elegans sex-determining gene tra-1 Hui et al, 1994, Dev. Biol. 162:402-13
  • Drosophila Ci is required for activation of hedgehog targets and also functions as a repressor of hedgehog expression.
  • GLIl, GLI2 and GLI3 may each carry out a specific function during vertebrate development (Kinzler et al. , 1984, Nature 332:371-374; Ruppert et al., 1988, Mo/. Cell. Biol. 8:3104-3113; Walterhouse ef ⁇ /., 1993, Dev. Dyn. 196:91-102; Hui et al., l994, Dev. Biol. 162:402-413).
  • Gli2 mutant mice exhibit severe skeletal abnormalities including cleft palate, tooth defects, absence of vertebral body and intervertebral discs, and shortened limbs and sternum (Mo et al, 1997, Development 124:113-23).
  • Gli3 represents an important control gene for development and differentiation of several body structures. For example, a reduction in gene dosage leads to severe
  • GLI3 Greig cephalopolydactyly syndrome (GCPS) affecting limb and craniofacial development and the autosomal dominant form of Pallister-Hall syndrome.
  • GCPS Greig cephalopolydactyly syndrome
  • GLI proteins function as transcriptional activators by binding via their zinc finger domains to a DNA binding site within a promoter and/or enhancer sequence of target genes.
  • DNA binding sequences bound by GLI proteins were identified.
  • the DNA sequence bound by GLI3 zinc fingers consists of 16 nucleotides and shows a high degree of similarity to sequences bound by the GLI and tra-1 proteins (Vortkamp et al, 1995, DNA Cell. Biol. 14:629-34).
  • This binding site included the 9-base- ⁇ air sequence 5 1 - GACCACCCA-3' previously identified for GLI protein binding (Kinzler and Vogelstein, 1990, MoI. Cell Biol 10:634-42).
  • GLI, GLI2, and GLI3 bind identical or similar DNA sequences (Yoon et al., 1998, J. Biol. Chem. 273:3496-3501). Recently, the 9 bp consensus sequence 5'-GACCACCCA-3' as a binding site for GLIl, GLI2, and GLI3 proteins was confirmed by Hallikas et al. (Hallikas et al, 2006, Cell 124:47-59). [0008] Activation of Hh/GLI target genes by GLI2 and GLI3 proteins may require the transcriptional c ⁇ -activator Creb Bing Protein (CBP), which binds to a CBP binding domain (see Fig. 1; Dai et al, 1999, J.
  • CBP transcriptional c ⁇ -activator Creb Bing Protein
  • GLI2 and GLI3 contain both activator and repressor domains (see Figure 1). GLI2 and GLI3 can be processed for different functions through the action of protein kinase A (PKA). Full-length GLI2 acts as a weak transcriptional activator.
  • PKA protein kinase A
  • Truncation of the activation domain in the C-terminal half results in a protein with repressor activity, while removal of the repression domain at the N-terminus converts GLI2 into a strong activator.
  • N-terminally truncated GLI2 unlike the full length protein, activates, for example a Sonic hedgehog (Shh) gene, HNF3beta, in transgenic mouse embryos. This suggested that unmasking the activation domain of GLI2 is one of the key mechanisms of the Shh signaling pathway.
  • Shh Sonic hedgehog
  • a similar regulatory mechanism involving the N-terminal region was also described for GLI3, but not for GLI. (Sasaki etal, 1999, Development 126:3915-24, incorporated by reference in its entirety).
  • a transcription activation domain for GLI was identified at the carboxy- terminus which comprised amino acid residues 1020 to 1091.
  • This domain includes an 18 amino acidic ⁇ -helix (amino acids 1037 to 1054) containing six aspartate or glutamate residues (Yoon et al., 1998, J. Biol. Chem. 273:3496-3501).
  • a similar domain is present in the other GLI family proteins.
  • putative TAF U 31 binding domains were described and include NH2-INKDNLRKDLFTVSIKA- COOH ⁇ rosophila Ci, amino acid residues 1044- 1060), NH 2 -DMADFEFEQMFTDALGI- COOH (VP 16, amino acid residues 469-485), NHa-DSLDLDNTQLDFVAILDE-COOH (human GLI, amino acid residues 1037-1054), NH 2 -DSLDLDNTQLDFVAILDE-COOH (mouse GLI, amino acid residues 1040-1057), NH 2 -DSHDLEGVQIDFDAIIDD-COOH (human GLI3, amino acid residues 1495-1512), and NH 2 -DSQLLEPPQIDFDAIMDD- COOH (mouse GLI2, amino acid residues 1509-1526).
  • putative TAFn31 interaction domains of human GLI2, NH 2 - DSQLLEAPQIDFDAIMDD-COOH (amino acid residues 1501-1518) can be identified, e.g., from GenBank Accession No. AAY87165.
  • putative TAFn31 interaction domain of mouse GLI3, NH 2 -ESHDLEGVQIDFDAIIDD-COOH (amino acid residues 1497-1514) can be identified from, e.g., GenBank Accession No. Q61602.
  • the conserved amino acid residues for contacting TAF ⁇ 31 are indicated in bold and underlined.
  • Hh-signaling in Drosophila and murine development, understanding of the molecular mechanisms and tumorigenic programs that are activated in response to Hh-signaling and GLI-activity in human cancer is still very limited.
  • a common property of Hh-associated cancers is the elevated expression level of one or more GLI proteins.
  • GLIl was found in a number of cancer types, including prostate, pancreas and small-cell lung cancer (Karhadkar et al, 2004, Nature 431 :707-12).
  • GIi was found to be amplified in childhood sarcomas and more than 50-fold in a malignant glioma (Roberts et al, 1989, Cancer Res.
  • Hedgehog Hedgehog
  • Ptch receptor Patched
  • GLI2 Basal cell carcinoma
  • BCC basal cell carcinoma
  • GLI2 and/or GLI3 might be more important in activation of Hh signaling during tumori genesis for many types of cancer, including lung cancer and prostate cancer.
  • Lung Cancer is the leading cause of cancer death in the United States and worldwide, with > 170,000 newly diagnosed cases each year in the United States and nearly a million cases worldwide (Minna et al, 2002, Cancer Cell. l(l):49-52). Despite aggressive approaches made in the therapy of lung cancer in the past decades, the 5-year survival rate for lung cancer remains under 15%. Lung cancers are divided into two groups: non-small-cell lung cancer (NSCLC) and small-cell lung cancer (SCLC). NSCLC (75-80% of all cancers) consists of three major types: adenocarcinoma, squamous cell carcinoma, and large cell carcinoma (Minna et al., 2002, Cancer Cell. 1(1 ):49-52). Lung carcinomas and squamous cell carcinomas represent 60-70% of all lung cancers. Surgery, chemotherapy, and radiation have been used with generally unsatisfactory results in advanced disease. Improvement in the efficacy of lung cancer treatment is a major public health goal.
  • Prostate cancer may be the most common solid tumor in men (Nelson et al, 2003, N. Engl. J. Med. 349:366-381). For example, 50% of all men over 50, and essentially all men over 70 suffer from some form of prostate hyperplasia. In the United States, prostate cancer is the most frequently diagnosed cancer, with over 250,000 new cases being diagnosed each year. 40,000 men die every year due to prostate cancer.
  • the inventors address a great and unfulfilled need in treating cancers wherein GLI proteins, and in particular GLI3, are overexpressed.
  • the present invention provides small molecule compounds, pharmaceutical compositions, kits and methods useful for the detection and treatment of a number of cancers wherein GLI3 protein is overexpressed.
  • Such cancers include lung cancer, NSCLC, breast cancer, colon cancer, mesothelioma, melanoma, sarcoma, prostate cancer, ovarian cancer, renal cancer, esophageal cancer, gastric cancer, hepatocellular cancer, nasopharyngeal cancer, pancreatic cancer, glioma, and others.
  • the activator domain of GLI3 protein (approximately 70 kDa) is overexpressed in various human cancer cell lines, including lung cancer, NSCLC, breast cancer, colon cancer, mesothelioma, melanoma, sarcoma, prostate cancer, ovarian cancer, renal cancer, esophageal cancer, gastric cancer, hepatocellular cancer, nasopharyngeal cancer, pancreatic cancer, glioma, and others.
  • Inhibition of GLI3 protein signaling can be achieved by different means, including but not limited to (i) direct inhibition of the transcriptional activity of GLI3 protein, (ii) inhibition of the processing of the GLI3 precursor protein, (iii) inhibition of phosphorylation of the GLI3 activator domain, or (iv) inhibition of any of the cellular proteins involved in the process of generating the active GLI3 protein.
  • Inhibition of GLI3 protein signaling can be accomplished by various means, for example by using small molecule compounds, siRNA, peptides, or antisense oligonucleotides. This invention provides small molecule compounds for inhibiting GLI protein signaling and in particular GLI3 protein signaling.
  • the present invention provides a small molecule compound of the formula:
  • each of X 1 and X 2 is independently N or C, wherein one of X 1 and X 2 is N and one of X 1 and X 2 is C, such that the ring N forms a double bond with whichever of X 1 and X 2 is C.
  • each of R 1 , R 2 and R 3 is independently selected from the group consisting of Ci-C( S alkylj aryl, heteroaryl, cycloalkyl and heterocycloalkyl, optionally substituted with 0-3 R 6 groups each independently selected from the group consisting of H, halogen, Cj -C ⁇ alkyl, -OR 7 , -C(O)R 7 , -OC(O)R 7 , -N(R 7 , R 7 ), -NR 7 S(O) 2 R 7 , -C(O)N(R 7 , R 7 ), -N(R 7 )C(O)R 7 , -N(R 7 )C(O)N(R 7 , R 7 ), -C(NR 7 )N(R 7 , R 7 ), -N(R 7 )C(NR 7 )N(R 7 , R 7 ), -N(R 7 )C(NR 7 )N(R 7 ,
  • Y is a direct bond or C 1 -C4 alkyl
  • Z is a member selected from the group consisting OfCj-C 4 alkyl, aryl and heteroaryl.
  • R 4 is H, halogen, -OR 7 , -OC(O)R 7 , -C(O)OR 7 , -N(R 7 , R 7 ), -NR 7 S(O) 2 R 7 , -C(O)N(R 7 , R 7 ), -N(R 7 )C(O)N(R 7 , R 7 ), -C(NR 7 )N(R 7 , R 7 ) and S(O) 1n R 7 wherein subscript m is O, 1 or 2.
  • R 5 is H, Ci -C ⁇ alkyl, or optionally combined with Y to form a 5 to 6 membered heterocycle.
  • Each R 7 is independently H or Ci- C 6 alkyl.
  • the present invention provides a small molecule compound of the formula where each of R 1 , R 2 and R 3 is aryl. In a further embodiment, each of R 1 , R 2 and R 3 is phenyl.
  • the present invention provides a small molecule compound of the formula where R 4 is hydroxy.
  • Z is C 1 -C 4 alkyl.
  • Z is aryl.
  • Z is phenyl.
  • the present invention provides a small molecule compound of the formula where each of R 1 , R 2 and R 3 is phenyl, where Y is Cj-C 4 alkyl, where Z is Cp C 4 alkyl or phenyl, and where R 4 is hydroxy.
  • the present invention provides a small molecule compound of the formula where X 1 is C and X 2 is N.
  • the small molecule compound of the formula has the following structure:
  • the small molecule compound of the formula has the following structure:
  • the present invention provides a small molecule compound of the formula where X 1 is N and X 2 is C.
  • the small molecule compound of the formula has the following structure:
  • the small molecule compound of the formula has the following structure:
  • the present invention also provides pharmaceutical compositions and medicaments.
  • the present invention provides a pharmaceutical composition comprising a small molecule compound of the present invention, and a pharmaceutically acceptable carrier.
  • the present invention also provides methods for using the small molecule compounds of the invention.
  • a method for inducing a tumor cell expressing a GLI protein to undergo apoptosis comprises the step of contacting the tumor cell with a small molecule compound of the invention in a sufficient amount, wherein the step of contacting results in inducing apoptosis in the tumor cell.
  • the GLI protein is GLI2 or GLD.
  • the small molecule compound is administered as part of a cancer treatment regimen.
  • a method for inhibiting at least one of unwanted growth, hyperproliferation, or survival of a cell comprises the step of determining whether the cell expresses a GK gene or alternatively a GLI protein. This method further comprises the step of contacting the cell with an effective amount of a small molecule of the present invention, wherein the step of contacting results in the inhibition of at least one of unwanted growth, hyperproliferation, or survival of the cell.
  • a cell or tumor cell useful in the methods of the present invention is selected from the group consisting of colon cancer, melanoma, mesothelioma, lung cancer, renal cell carcinoma, breast cancer, prostate cancer, sarcoma, ovarian cancer, esophageal cancer, gastric cancer, hepatocellular cancer, nasopharyngeal cancer, pancreatic cancer, and glioma cell.
  • Methods of the present invention can be practiced in vitro or in vivo.
  • a method for treating a subject suffering from a cancerous condition comprises the step of administering to the subject a therapeutically effective amount of a small molecule compound, wherein the cancerous condition is characterized by expressing a GLI polypeptide, preferably a GLI3 polypeptide and wherein the step of administering results in the treatment of the subject.
  • a method for inhibiting the activity of a GLI protein in a cell is provided.
  • This method comprises the step of contacting the cell with a small molecule compound of the present invention, wherein the step of contacting results in the inhibition of the activity of the GLI protein in the cell.
  • a preferred GLI protein activity that is inhibited is a protein-protein interaction between a GLI protein and a cellular protein or a nuclear protein.
  • a preferred nuclear protein is a TAF protein, a TATA-Box Binding Protein Associated Factor, preferably a TAF ⁇ 31 protein.
  • the present invention provides a method for inhibiting the expression of a gene having a GLI DNA binding site operably linked to the promoter of the gene.
  • This method comprises the step of contacting a cell expressing the gene having a GLI DNA binding site operably linked to its promoter with a small molecule compound of the present invention, wherein the step of contacting results in inhibition of expression of the gene.
  • the gene is a Wnt2 gene and preferably a human Wnt2 gene.
  • the present invention provides for the use of a small molecule compound of the present invention in the manufacture of a medicament for inhibiting at least one of unwanted growth, hyperproliferation, or survival of a cell.
  • a use of a small molecule compound in the manufacture of a medicament for treatment of a cancer is provided.
  • the present invention provides for the use of a small molecule compound in the manufacture of a medicament for inducing apoptosis in a cell.
  • the present invention provides screening methods.
  • a preferred method of this invention is a method for identifying a candidate compound capable of inhibiting the protein-protein interaction between a GLI protein and a TAFn31 protein.
  • this method comprises the steps of contacting a candidate compound with a sample comprising a GLI protein and a TAF ⁇ 31 protein; and determining the binding of the GLI-protein to the TAF ⁇ 31 protein.
  • a reduced binding of the GLI protein to the TAF ⁇ 31 in the presence of the candidate compound compared to the binding of the GLI protein to the TAF U 31 in the absence of the candidate compound indicates that the candidate compound is capable of inhibiting the interaction between the GLI protein and the TAF ⁇ 31 protein.
  • Another method provided herein is a method for identifying a compound that modulates a GLI protein activity.
  • the GLI protein activity is GLI protein dependent transcription activity and the method is for identifying a compound that modulates GLI protein dependent transcription activity.
  • the method comprises the steps of contacting a sample with a candidate compound, wherein the sample comprises an expression reporter construct having one or more GLI DNA binding sites operably linked to a reporter gene; and determining the effect, if any, of the candidate compound on the level of GLI protein dependent transcription activity.
  • Figure 1 shows the location of the transcription activation domain of GLD.
  • GLI3 transcription activation domain is located near the C-terminus and contains a conserved VP 16-like activating region (TAFn31 binding domain), and is necessary for the activator function of GLI3, but not for the repressor function of GLI3.
  • TAFn31 binding domain conserved VP 16-like activating region
  • This FXX ⁇ motif is thought to contact TAFu31 directly, hi GLI3, this domain has the amino acid sequence FDAII.
  • Figure 2 shows a semi-quantitative RT-PCR analysis to demonstrate detection of Gli3 expression in human cell lines.
  • the upper panel of this figure shows a schematic representation of GLI3 showing the repression domain (amino acid residues 1-397), the Zinc finger domain (amino acid residues 482-637) and the CBP-binding domain (amino acid residues 827-1132).
  • the approximate location of PCR primers F2 and R2 is indicated (see Table 1 for details).
  • the middle panel of this figure shows the following cell lines analyzed by RT-PCR: normal liver (lane 1); NSCLC: H1703, H460 and A549 (lanes 2- 4); breast cancer: HuLlOO, BT474 and MCF-7 (lanes 5-7); mesothelioma: Met5A, H290, REN, H513, H28, 21 IH, and LARKlA (lanes 8-14); colon cancer: SW480 (lane 15); a pair of primary NSCLC tissue samples (lanes 16 and 17 are normal and cancer tissues, respectively).
  • the lower panel of this figure shows the following cell lines analyzed by RT-PCR: Colon cancer: SW480, HCTl 16, HT29, Lovo and CaCO2 (lanes 1-5); normal colon (lane 6); normal renal cell lines: HRE- 152 and HK-2 (lanes 7 and 8); renal cell carcinoma: 786-Om Caki, 769-P, A704 and OMRC3 (lanes 9-13); normal lung (lane 14); mesothelioma: REN, H290, 21 IH, H513, H2052, H28 and MS-I (lanes 15-21); NSCLC: A549, H460, H838, H1703, H1229, H1650, H1975, and A427 (lanes 22-29). Most cancer cell lines and the primary tissue samples express Gli3. Notably, no Gli3 expression is detected in colon cancer cell line HT29 (lower panel, lane 2). Details are described in Example 4.
  • FIG. 3 shows a manually generated RMS overlay between the small molecule compound FNl -5 and the FXX ⁇ motif for GLB (amino acid sequence: FDAII).
  • the FDAII is shown as an alpha-helix. Details are described, e.g., in Example 2.
  • Figure 4 shows an initial screening of small molecule compounds FNl-I, FN 1-2, FN1-3, FN1-5, and FN2-1.
  • the small molecule compounds were designed to inhibit the GLI3 transcription activation (TAF-binding domain). Dramatic killing of all cancer cells tested is observed with small molecule compound FN 1-5.
  • DMSO was used as a control. Details are described, e.g., in Example 5.
  • Figure 5 shows a flow cytometry analysis demonstrating that small molecule compound FN 1-5 induces apoptosis in the colon cancer cell line SW480. Significant apoptosis (58.6%) was observed at 100 ⁇ M FNl -5, consistent with the staining result.
  • Figure 6 shows the screening of small molecule compounds FN1-7, FN1-8, and FN3-5 using a cytotoxicity assay and the NSCLC cell lines Hl 299, A549, and H460, as described herein. Dramatic cell killing was observed in all cancer cells that were treated with small molecule compound FN1-8. Details are described, e.g., in Example 5.
  • Figure 7 shows the result of a cytotoxicity assay after treating LOX cells
  • Figure 8 shows the effect of different small molecule compounds on primary cultured human mesothelioma cells freshly made from tissue samples. Dramatic cell killing effect was observed for both FN1-5 and FN1-8. Small molecule compound FN1-8 was more potent than FN1-5 in killing this primary culture at the same dose. DMSO was used as a control. Details are described, e.g., in Example 11.
  • Figure 9 shows regulation in the NSCLC cell line A549 of Wnt2 promoter activity by small molecule compounds FNl-I, FN1-2, FN1-3, FNl -5, FNl -7, FN1-8, FN2-1, FN2-5, and FN3-5. Both FN 1-5 and FN 1-8 down-regulate Wnt2 promoter activity dramatically.
  • DMSO and "Empty vector" are controls. Details are described, e.g., in Example 27.
  • Figure 10 shows regulation of the TOP/FOP activity in the colon cancer cell line HCTl 16 by small molecule compounds FN1-5, FN1-7, FN1-8, FN1-9U, FN1-9S, FN2-1, and FN3-5. Both FN1-5 and FN1-8 were found to down-regulate TOP/FOP activity dramatically. DMSO was used as a control. Details are described, e.g., in Example 31.
  • Figure 11 shows that small molecule compounds FN 1-5 and FN 1-8 do not regulate SOCS3 promoter activity in NSCLC A549 cells. Empty vector and DMSO serve as controls. Details are described, e.g., in Example 32.
  • Figure 12 shows a Western blot analysis of Dvl-3, cytosolic beta-catenin, Survivin and actin (control) in colon cancer cells after treatment with FN1-5 and FN1-8.
  • the small molecule compounds FN1-5 and FN1-8 suppress canonical Wnt signaling in colon cancer cells. Details are described, e.g., in Example 33.
  • Figure 13 shows a Western blot analysis of Dvl-3, cytosolic beta-catenin, Survivin and actin (control) in NSCLC cells after treatment with FN1-5 and FN1-8.
  • the small molecule compounds FN1-5 and FN1-8 suppress canonical Wnt signaling in NSCLC cells. Details are described, e.g., in Example 33.
  • Figure 14 shows the result of a time course experiment demonstrating that FN 1-8 induces significant apoptosis in Malme-3M cells (A), A375 cells (B), and SK-Mel-5 cells (C), but not in human normal skin fibroblast cells (D). Details are described in Example 10.
  • Figure 15 shows that small molecule compound FN1-8 down-regulates GLIl- induced transcription activity in the melanoma cell lines Malme-3M (A), A375 (B) 3 SK-MeI- 2 (C), and SK-Mel-5 (D). Details are described in Example 29.
  • Figure 16 shows that small molecule compound FNl -8 reduces GLI protein-TAF- induced transcriptional activation in the NSCLC cell line A549. Details are described in Example 35.
  • Figure 17 shows the in vivo efficacy of small molecule compound FN 1-8 in mouse Xenograft Models NSCLC H460 (arrows) and melanoma LOX (arrow heads). Tumor growth is significantly suppressed after treatment with FNl -8. Details are described, e.g., in Examples 36 and 37.
  • Figure 18 shows an in vivo efficacy study of small molecule compound FN 1-8 using a Mouse Xenograft Model (NSCLC H460).
  • Arrows indicate daily injection of small molecule compound FNl -8 or DMSO as a control (each two times for 6 consecutive days). B.
  • FIG 19 shows an in vivo efficacy study of small molecule compound FN 1-8 using a Mouse Xenograft Model (Melanoma LOX).
  • Figure 20 shows an in vivo efficacy study of small molecule compound FN 1-8 using a Mouse Xenograft Model (Colon Cancer HT29). See, Example 35 for details.
  • B. Tumor weight after treatment with FNl -8 is similar to the DMSO control group. Results are the means ⁇ SD (error bars). Details are described, e.g., in Example 38.
  • Figure 21 shows a pharmacokinetic analysis of small molecule compounds FN 1 -5 (A) and FNl -8 (B) in mice (i.p. injection). Results are presented as mean values of the data obtained from three mice with SD (error bars). Details are described in Example 43.
  • Figure 22 shows a pharmacokinetic analysis of small molecule compounds FN 1-5 (A) and FNl -8 (B) in mice (oral administration). Results are presented as mean values of the data obtained from three mice with SD (error bars). Details are described in Example 43. [0061] Figure 23 shows the quantification ofa co-immunoprecipitation analysis
  • the binding was interfered by FN 1-8 in dose-dependent manner: the binding for GLIl -T AFbd was 73.6% and 33.5%, forGLI2-TAFbd was 73.8% and 60%, for GLI3-TAFbd was 71.6% and 28.6%, after treatment with 20 ⁇ M and 50 ⁇ M FN1-8, respectively. Details are described in
  • alkyl refers to a straight or branched chain hydrocarbon radical, and can include di- and multivalent radicals, having the number of carbon atoms designated (i.e. Ci-C 1O means one to ten carbons).
  • saturated hydrocarbon radicals include groups such as methyl, ethyl, n-propyl, isopropyl, n-butyl, t-butyl, isobutyl, sec-butyl, homologs and isomers of, for example, n-pentyl, n-hexyl, n-heptyl, n-octyl, and the like.
  • alkenyl refers to an unsaturated alkyl group one having one or more double bonds.
  • alkenyl groups include vinyl, 2-propenyl, crotyl, 2- isopentenyl, 2-(butadienyl), 2,4-pentadienyl and 3-(l,4-pentadienyl), and the higher homologs and isomers.
  • alkynyl refers to an unsaturated alkyl group one having one or more triple bonds.
  • alkynyl groups include ethynyl (acetylenyl), 1 - propynyl, 1- and 2-butynyl, and the higher homologs and isomers.
  • amino acid refers to naturally occurring and synthetic amino acids, as well as amino acid analogs and amino acid mimetics that function similarly to the naturally occurring amino acids. Naturally occurring amino acids are those encoded by the genetic code, as well as those amino acids that are later modified, e.g., hydroxyproline, ⁇ - carboxyglutamate, and O-phospho serine.
  • amino acid analog refers to a compound that has the same basic chemical structure as a naturally occurring amino acid, e.g., an ⁇ carbon that is bound to a hydrogen, a carboxyl group, an amino group, and an R group, e.g., homoserine, norleucine, methionine sulfoxide, methionine methyl sulfonium. Such analogs may have modified R groups (e.g., norleucine) or modified peptide backbones, but retain the same basic chemical structure as a naturally occurring amino acid.
  • Amino acid mimetic refers to a chemical compound that has a structure that is different from the general chemical structure of an amino acid, but that functions similarly to a naturally occurring amino acid.
  • Amino acids may be referred to herein by either their commonly known three letter symbols or by the one-letter symbols recommended by the IUPAC-IUB Biochemical Nomenclature Commission. Nucleotides, likewise, may be referred to by their commonly accepted single-letter codes.
  • aryl refers to a polyunsaturated, aromatic, hydrocarbon substituent having 5-12 ring members, which can be a single ring or multiple rings (up to three rings) which are fused together or linked covalently.
  • Non-limiting examples of aryl groups include phenyl, 1-naphthyl, 2-na ⁇ hthyl, 4-biphenyl, and benzyl. Other aryl groups are also useful in the present invention.
  • Bio sample as used herein is a sample of biological tissue or fluid that contains nucleic acids or polypeptides. Such samples are typically from humans, but include tissues isolated from non-human primates, or rodents, e.g., mice, and rats. Biological samples may also include sections of tissues such as biopsy and autopsy samples, frozen sections taken for histological purposes, blood, plasma, serum, sputum, stool, tears, mucus, hair, skin, etc. Biological samples also include explants and primary and/or transformed cell cultures derived from patient tissues. A “biological sample” also refers to a cell or population of cells or a quantity of tissue or fluid from an animal.
  • biological sample can also refer to cells or tissue analyzed in vivo, i.e., without removal from the animal.
  • a biological sample will contain cells from the animal, but the term can also refer to noncelMar biological material, such as noncellular fractions of blood, saliva, or urine, that can be used to measure the cancer-associated polynucleotide or polypeptide levels.
  • noncelMar biological material such as noncellular fractions of blood, saliva, or urine.
  • Numerous types of biological samples can be used in the present invention, including, but not limited to, a tissue biopsy, a blood sample, a buccal scrape, a saliva sample, or a nipple discharge.
  • tissue biopsy refers to an amount of tissue removed from an animal, preferably a human, for diagnostic analysis. In a patient with cancer, tissue may be removed from a tumor, allowing the analysis of cells within the tumor.
  • tissue biopsy can refer to any type of biopsy, such as needle biopsy, fine needle biopsy, surgical biopsy, etc.
  • Providing a biological sample means to obtain a biological sample for use in methods described in this invention. Most often, this will be done by removing a sample of cells from a patient, but can also be accomplished by using previously isolated cells (e.g., isolated by another person, at another time, and/or for another purpose), or by performing the methods of the invention in vivo. Archival tissues, having treatment or outcome history, will be particularly useful.
  • Cancer cells “transformed” cells or “transformation” in tissue culture, refers to spontaneous or induced phenotypic changes that do not necessarily involve the uptake of new genetic material.
  • transformation can arise from infection with a transforming virus and incorporation of new genomic DNA, or uptake of exogenous DNA, it can also arise spontaneously or following exposure to a carcinogen, thereby mutating an endogenous gene. Transformation is associated with phenotypic changes, such as immortalization of cells, aberrant growth control, nonmorphological changes, and/or malignancy (see, Freshney, Culture of Animal Cells a Manual of Basic Technique (3rd ed. 1994)).
  • change in cell growth refers to any change in cell growth and proliferation characteristics in vitro or in vivo, such as formation of foci, anchorage independence, semi-solid or soft agar growth, changes in contact inhibition and density limitation of growth, loss of growth factor or serum requirements', changes in cell
  • Correlating the amount means comparing an amount of a substance, molecule or marker (such as GIi or GLI) that has been determined in one sample to an amount of the same substance, molecule or marker determined in another sample.
  • the amount of the same substance, molecule or marker determined in another sample may be specific for a given cancer.
  • determining the amount include, but are not limited to, detecting, measuring, testing or determining, the presence, absence, amount or concentration of a molecule, such as GIi or GLI.
  • cycloalkyl refers to a saturated cyclic hydrocarbon having 3 to 15 carbons, and 1 to 3 rings that can be fused or linked covalently.
  • Cycloalkyl groups useful in the present invention include, but are not limited to, cyclopentyl, cyclohexyl, cycloheptyl and cyclooctyl.
  • Bicycloalkyl groups useful in the present invention include, but are not limited to, [3.3.0]bicyclooctanyl, [2.2.2Jbicyclooctanyl, [4.3.0]bicyclononane,
  • cycloalkenyl refers to an unsaturated cyclic hydrocarbon having 3 to 15 carbons, and 1 to 3 rings that can be fused or linked covalently.
  • Cycloalkenyl groups useful in the present invention include, but are not limited to, cyclopentenyl, cyclohexenyl, cycloheptenyl and cyclooctenyl. Bi cycloalkenyl groups are also useful in the present invention.
  • determining the functional effect is meant assaying for a compound that increases or decreases a parameter that is indirectly or directly under the influence of a GLI protein, e.g., functional, enzymatic, physical and chemical effects. Such functional effects can be measured by any means known to those skilled in the art, e.g., changes in
  • spectroscopic characteristics ⁇ e.g., fluorescence, absorbance, refractive index), hydrodynamic ⁇ e.g., shape), chromatographic, or solubility properties for the protein, measuring inducible markers or transcriptional activation of the GLI protein; measuring binding activity, e.g., binding to a TAF protein (e.g., TAF ⁇ 31), measuring cellular proliferation, measuring apoptosis, or the like.
  • Determination of the functional effect of a compound, e.g., a small molecule compound, on cancer can also be performed using assays known to those of skill in the art such as an in vitro assays, e.g., cell growth on soft agar; anchorage dependence;
  • transformation transformation; growth factor or serum dependence; tumor specific marker levels;
  • RNA and protein expression in cells undergoing metastasis and other characteristics of cancer cells.
  • the functional effects can be evaluated by many means known to those skilled in the art, e.g., microscopy for quantitative or qualitative measures of alterations in morphological features, measurement of changes in GIi RNA or protein levels, measurement of RNA stability, identification of down-stream or reporter gene expression (CAT, luciferase, ⁇ -gal, GFP and the like), e.g., via chemiluminescence, fluorescence, colorimetric reactions, antibody binding, inducible markers, and ligand binding assays.
  • “Functional effects” include in vitro, in vivo, and ex vivo activities.
  • determining are contemplated within the scope of the present invention and include, but are not limited to, detecting, measuring, assaying, testing or determining, the presence, absence, amount or concentration of a molecule, such as a GLI polypeptide, a label, a small molecule compound of the invention.
  • the term refers to both qualitative and quantitative determinations.
  • down-regulate or “inhibiting” in the context of Shh signaling , GLI signaling, or Wnt2 signaling refers to partially or totally block Shh signaling , GLI signaling, or Wnt2 signaling as measured by known assays for Shh signaling , GLI signaling, or Wnt2 signaling.
  • Inhibitors for example, are small molecule compounds of the present invention.
  • an "effective amount”, “effective dose”, “sufficient amount” or grammatical equivalents thereof of a small molecule compound of the present invention for treatment is an amount that is sufficient to ameliorate, or in some manner, reduce a symptom or stop or reverse progression of a condition.
  • Amelioration of a symptom of a particular condition, e.g., cancer, by administration of a particular pharmaceutical composition refers to any lessening, whether permanent or temporary, lasting or transit that can be associated with the
  • an "effective amount” can be any amount of the pharmaceutical composition.
  • an "expression vector” or “expression construct” is a nucleic acid construct, generated recombinantly or synthetically, with a series of specified nucleic acid elements that permit transcription of a particular nucleic acid in a host cell.
  • the expression vector can be part of a plasmid, virus, or nucleic acid fragment.
  • the expression vector includes a nucleic acid to be transcribed operably linked to a promoter.
  • GLI refers to a family of GLI proteins. GLI proteins include GLI (also referred to as GLIl), GLI2, and GLI3. A preferred GLI protein is GLIl, GLI2, or GLI3.
  • GLIi refers to a gene encoding a GLI protein.
  • GHl , GH2, and Gli3 are genes encoding a GLIl, GLI2 and GLI3 protein, respectively.
  • GLI protein activity refers to GLI signaling and includes, for example,
  • GLI Gene binding protein
  • binding of GLI protein to a GLI DNA binding site and binding of GLI protein to other proteins, e.g., a TAF or to co- activators, such as CBP (Creb Protein Binding Protein).
  • CBP Cell Binding Protein
  • GLI DNA binding site refers to a nucleotide sequence to which a GLI protein binds and from which it can activate gene transcription. GLI DNA binding sites were described by, e.g., Vortkarnp et al. (1995, DNA Cell. Biol. 14:629-34) Kinder and Vogelstein (1990, MoI. Cell. Biol. 10:634-42) and Yoon et al. (998, J Biol Chem 273:3496-3501).
  • GLI DNA binding site bound by GLI3 zinc fingers described by Vortkamp et al. (1995, DNA Cell. Biol. 14:629-34), for example, consists of 16 nucleotides and shows a high degree of similarity to sequences bound by the GLI and tra-1 proteins. This binding site included the 9- base-pair sequence 5'-GACCACCCA-3'. It is understood that a GLI3 DNA binding site need not be 100% identical to the GLI DNA binding site identified by Vortkamp et al. (1995, DNA Cell. Biol. 14:629-34). For example, recently, Hallikas et al.
  • GLIl, GLI2, and GLI3 determined the DNA binding specificities of GLIl, GLI2, and GLI3 and also found GLI binding to, for example, 5'- TACCAACCC A-3', 5'-GCCCACCCA-S 1 , 5'-GGCCACCCA-3', and 5 r -GATCACCCA-3 f , wherein the underlined nucleotide indicates a difference to the 9 bp consensus sequence (Hallikas et al., 2006, Cell 124(l):47-59; incorporated by reference in its entirety).
  • Assays to determine binding of a GLI protein to a GLI DNA binding site are known in the art and include, e.g., electrophoretic mobility shift assays (EMSA; Fried and Crothers, 1981, Nucleic Acids Res. 9:6505-6525; Hallikas et al., 2006, Cell 124:47-59) SELEX (Roulet et al., 2002 Nat. Biotechnol. 20:831-835) , and chromatographic binding assays.
  • a "GLI" polypeptide includes both naturally occurring or recombinant forms.
  • a GLI polypeptide and a GLI subdomain polypeptide as described herein can comprise a sequence that corresponds to a human GLI sequence.
  • exemplary GLI are provided herein and are known in the art.
  • several vertebrate GLIl, GLI2, and GLI3 proteins have been characterized, for example, human GLIl
  • NM_001034190, AY665272, Q5IS56 mouse GLI3 (GenBank Accession Nos. X95255, NM_008130, NP_032156, Q61602), rat GLI3 (GenBank Accession No. XMJ225411 ), zebrafish GLI3 (GenBank Accession Nos.
  • a GLI protein may be a full-length GLI protein or it may be a partial GLI protein, such as a subdomain of a GLI protein.
  • a "GLI3" polypeptide refers to a polypeptide and polymorphic variants, alleles, mutants of human GLI3 that: (i) has an amino acid sequence that has greater than about 60% amino acid sequence identity, 65%, 70%, 75%, 80%, 85%, 90%, preferably 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% or greater amino acid sequence identity, preferably over a region of at least about 100, 150, 200, 250, 300, 500 or more amino acids, to a human GLI3 selected from GenBank Accession Nos.
  • a "GIi nucleic acid” or “gli polynucleotide” refers to a vertebrate gene encoding a GLI, GLI2, or GLI3 protein.
  • a "GIi nucleic acid” includes both naturally occurring or recombinant forms.
  • a GH polynucleotide or GLI polypeptide encoding sequence is typically from a human, but may be from other mammals, but not limited to, a non-human primate, a rodent, e.g., a rat, mouse, or hamster; a cow, a pig, a horse, a sheep, or other mammal.
  • GIi nucleic acids useful for practicing the present invention have been cloned and characterized, for example, human Glil (GenBank Accession Nos. NM_OO5269), mouse Glil (GenBank Accession Nos. NM_010296, AB025922), zebrafish Glil (GenBank Accession No.
  • NM__178296 human Gli2 (GenBank Accession Nos. NM_O3O381; NM_O3O38O; NM- 030379, DQ086814), mouse GH2 (GenBank Accession No .XM_922107), human GH3 (GenBank Accession Nos. NM_000168, AJ250408, M57609), chimpanzee Gli3 (GenBank Accession Nos. NMJ)Ol 034190, AY665272), mouse GH3 (GenBank Accession Nos.
  • a GIi polynucleotide may be a full- length GH polynucleotide, i.e., encoding a complete GLI protein or it may be a partial GIi polynucleotide encoding a subdomain of a GLI protein.
  • the terms "GLI pathway”, “GLI signaling” or “GLI signaling pathway” are used interchangeably and refer to the signaling pathway initiated by a hedgehog protein binding to its receptor(s) leading to the expression and/or activity of a GLI protein.
  • halogen refers to the elements including fluorine (F), chlorine (Cl), bromine (Br) and iodine (I).
  • Hh hedgehog
  • Hh a cytokine that binds to a Hh receptor thereby initiating the Hh signaling pathway leading to the expression or activation of GLI proteins.
  • Sonic hedgehog Sonic hedgehog
  • Ihh Indian hedgehog
  • Dhh Desert hedgehog
  • Several vertebrate hedgehog proteins are known in the art, for example, human SHH, murine SHH, rat SHH, human IHH, and murine DHH.
  • heteroaryl refers to a polyunsaturated, aromatic, hydrocarbon substituent having 5-12 ring members, which can be a single ring or multiple rings (up to three rings) which are fused together or linked covalently, and which has at least one heteroatom in the ring, such as N, O, or S.
  • a heteroaryl group can be attached to the remainder of the molecule through a heteroatom.
  • heteroaryl groups include 1-pyrrolyl, 2-pyrrolyl, 3-pyrrolyl, 3-pyrazolyl, 2-imidazolyl, 4-imidazolyl, pyrazinyl, 2-oxazolyl, 4-oxazolyl, 2-phenyl-4-oxazolyl, 5-oxazolyl, 3-isoxazolyI, 4- isoxazolyl, 5-isoxazolyl, 2-thiazolyl, 4-thiazolyl, 5-thiazolyl, 2-furyl, 3-furyl, 2-thienyl, 3- thienyl, 2-pyridyl, 3-pyridyl, 4-pyridyl, 2-pyrimidyi, 4-pyrimidyl, 5-benzothiazolyl, purinyl, 2-benzimidazolyl, 5-indolyl, 1-isoquinolyl, 5-isoquinolyl, 2-quinoxalinyl, 5-quinoxalinyl, 3- quinolyl, and 6-quino
  • Additional heteroaryl groups useful in the present invention include pyridyl N-oxide, tetrazolyl, benzofuranyl, benzothienyl, indazolyl, or any of the radicals substituted, especially mono- or di-substituted.
  • heterocycloalkyl refers to a saturated cyclic hydrocarbon having 3 to 15 ring members, and 1 to 3 rings that can be fused or linked covalently, and which has at least one heteroatom in the ring, such as N, O, or S. Additionally, a heteroatom can occupy the position at which the heterocycle is attached to the remainder of the molecule.
  • heterocycloalkyl include 1 -(1,2,5,6-tetrahydropyridyl), 1-piperidinyl, 2- piperidinyl, 3-piperidinyl, 4-morpholinyl, 3-morpholinyl, tetrahydrofuran-2-yl,
  • a "label” or a "detectable moiety” is a composition detectable by spectroscopic, photochemical, biochemical, immunochemical, chemical, or other physical means.
  • useful labels include 3 H, 125 1, 32 P, fluorescent dyes, electron-dense reagents, enzymes (e.g., as commonly used in an ELISA), biotin, digoxigenin, or haptens and proteins or other entities which can be made detectable, e.g., by incorporating a radiolabel into a small molecule compound.
  • the labels may be incorporated into a small molecule compound at any position.
  • level of GIi mRNA or “level of Wnt2 mRNA” in a biological sample refer to the amount of mRNA transcribed from a GIi or Wnt gene, respectively, that is present in a cell or a biological sample.
  • the mRNA generally encodes a functional GLI or WNT protein, although mutations may be present that alter or eliminate the function of the encoded protein.
  • a "level of GIi mRNA” or “level of Wnt2 mRNA” need not be quantified, but can simply be detected, e.g., a subjective, visual detection by a human, with or without comparison to a level from a control sample or a level expected of a control sample.
  • the "level of GLI polypeptide” or “level of Wnt2 polypeptide” in a biological sample refers to the amount of polypeptide translated from a GIi or Wnt2 mRNA
  • the polypeptide may or may not have GLI or WNT2 protein activity.
  • a "level of GLI polypeptide” or “ WNT2 polypeptide” need not be quantified, but can simply be detected, e.g., a subjective, visual detection by a human, with or without comparison to a level from a control sample or a level expected of a control sample.
  • a "modulator" of the level or activity of a polypeptide such as a GLI includes an activator and/or inhibitor of that polypeptide and is used to refer to compounds that activate or inhibit the level of expression of the polypeptide or the activity of the polypeptide.
  • Preferred polypeptides are GLIl, GLI2, or GLI3.
  • Activators are compounds that, e.g., induce or activate the expression of a polypeptide of the invention or bind to, stimulate, increase, open, activate, facilitate, or enhance activation, sensitize or up regulate the activity of a polypeptide of the invention.
  • Activators include naturally occurring and synthetic compounds, small chemical molecules and the like.
  • Assays for activators include, e.g.
  • Samples or assays comprising a GLI polypeptide that are treated with a potential activator are compared to control samples without the activator to examine the extent of effect.
  • Control samples (untreated with candidate compounds) are assigned a relative activity value of 100%.
  • Activation of the polypeptide is achieved when the polypeptide activity value relative to the control is 110%, optionally 130%, 150%, optionally 200%, 300%, 400%, 500%, or 1000-3000% or more higher.
  • Inhibitors are compounds that, e.g., repress or inactivate the expression of a polypeptide of the invention or bind to, decrease, close, inactivate, impede, or reduce activation, desensitize or down regulate the activity of a polypeptide of the invention.
  • Inhibitors include nucleic acids such as siRNA and antisense RNA that interfere with the expression of a GLI protein, as well as naturally occurring and synthetic compounds, small chemical molecules and the like.
  • Assays for inhibitors are described herein. Samples or assays comprising a GLI polypeptide that are treated with a potential inhibitor are compared to control samples without the inhibitor to examine the extent of effect. Control samples (untreated with candidate compounds) are assigned a relative activity value of 100%. Inhibition of the polypeptide is achieved when the polypeptide activity value relative to the control is reduced by 10%, optionally 20%, optionally 30%, optionally 40%, optionally 50%, 60%, 70%, 80%, or 90-100%.
  • the term "pharmaceutically acceptable 11 means approved by a regulatory agency of a Federal or state government or listed in the U.S. Pharmacopeia or other generally recognized pharmacopeia for use in animals, and more particularly in humans.
  • polypeptide peptide
  • protein protein
  • amino acid polymers in which one or more amino acid residue is an artificial chemical mimetic of a corresponding naturally occurring amino acid, as well as to naturally occurring amino acid polymers, those containing modified residues, and non-naturally occurring amino acid polymer.
  • prodrug refers to compounds that readily undergo chemical changes under physiological conditions to provide the compounds of the present invention. Additionally, prodrugs can be converted to the compounds of the present invention by chemical or biochemical methods in an ex vivo environment. For example, prodrugs can be slowly converted to the compounds of the present invention when placed in a transdermal patch reservoir with a suitable enzyme or chemical reagent.
  • a “promoter” is defined as an array of nucleic acid control sequences that direct transcription of a nucleic acid.
  • a promoter includes necessary nucleic acid sequences near the start site of transcription, such as, in the case of a polymerase II type promoter, a TATA element.
  • a promoter also optionally includes distal enhancer or repressor elements, which can be located as much as several thousand base pairs from the start site of transcription.
  • “constitutive” promoter is a promoter that is active under most environmental and developmental conditions.
  • An “inducible” promoter is a promoter that is active under environmental or developmental regulation.
  • the term “operably linked” refers to a functional linkage between a nucleic acid expression control sequence (such as a promoter, or array of transcription factor binding sites) and a second nucleic acid sequence, wherein the expression control sequence directs transcription of the nucleic acid corresponding to the second sequence.
  • recombinant when used with reference, e.g., to a cell, or nucleic acid, protein, or vector, indicates that the cell, nucleic acid, protein or vector, has been modified by the introduction of a heterologous nucleic acid or protein or the alteration of a native nucleic acid or protein, or that the cell is derived from a cell so modified.
  • recombinant cells express genes that are not found within the native (non-recombinant) form of the cell or express native genes that are otherwise abnormally expressed, under expressed or not expressed at all.
  • nucleic acid By the term “recombinant nucleic acid” herein is meant nucleic acid, originally formed in vitro, in general, by the manipulation of nucleic acid, e.g., using polymerases and endonucleases, in a form not normally found in nature. In this manner, operably linkage of different sequences is achieved.
  • an isolated nucleic acid, in a linear form, or an expression vector formed in vitro by ligating DNA molecules that are not normally joined are both considered recombinant for the purposes of this invention.
  • a recombinant nucleic acid is made and reintroduced into a host cell or organism, it will replicate non-recombinantly, i.e., using the in vivo cellular machinery of the host cell rather than in vitro manipulations; however, such nucleic acids, once produced recombi ⁇ antly, although subsequently replicated non-recombinantly, are still considered recombinant for the purposes of the invention.
  • a "recombinant protein” is a protein made using recombinant techniques, i.e., through the expression of a recombinant nucleic acid as depicted above.
  • resistant to chemotherapeutic agents herein is meant a tumor that does not respond to treatment with a chemotherapeutic agent, i.e., is not killed by, or growth-inhibited by, such treatment.
  • salts refers to salts of the active compounds which are prepared with relatively nontoxic acids or bases, depending on the particular substituents found on the compounds described herein.
  • base addition salts can be obtained by contacting the neutral form of such compounds with a sufficient amount of the desired base, either neat or in a suitable inert solvent.
  • pharmaceutically acceptable base addition salts include sodium, potassium, calcium, ammonium, organic amino, or magnesium salt, or a similar salt.
  • acid addition salts can be obtained by contacting the neutral form of such compounds with a sufficient amount of the desired acid, either neat or in a suitable inert solvent.
  • Examples of pharmaceutically acceptable acid addition salts include those derived from inorganic acids like hydrochloric, hydrobromic, nitric, carbonic, monohydrogencarbonic, phosphoric, monohydrogenphosphoric, dihydrogenphosphoric, sulfuric, monohydrogensulfuric, hydriodic, or phosphorous acids and the like, as well as the salts derived from relatively nontoxic organic acids like acetic, propionic, isobutyric, maleic, malonic, benzoic, succinic, suberic, fumaric, mandelic, phthalic, benzenesulfonic, p-tolylsulfonic, citric, tartaric, methanesulfonic, and the like.
  • inorganic acids like hydrochloric, hydrobromic, nitric, carbonic, monohydrogencarbonic, phosphoric, monohydrogenphosphoric, dihydrogenphosphoric, sulfuric, monohydrogensulfuric, hydriodic, or phosphorous acids and the like,
  • salts of amino acids such as arginate and the like, and salts of organic acids like glucuronic or galactunoric acids and the like (see, for example, Berge, S.M., et al, "Pharmaceutical Salts", Journal of Pharmaceutical Science, 1977, 66, 1-19).
  • Certain specific compounds of the present invention contain both basic and acidic functionalities that allow the compounds to be converted into either base or acid addition salts.
  • the neutral forms of the compounds may be regenerated by contacting the salt with a base or acid and isolating the parent compound in the conventional manner.
  • the parent form of the compound differs from the various salt forms in certain physical properties, such as solubility in polar solvents, but otherwise the salts are equivalent to the parent form of the compound for the purposes of the present invention.
  • solvates refers to compounds of the present invention that are complexed to a solvent.
  • Solvents that can form solvates with the compounds of the present invention include common organic solvents such as alcohols (methanol, ethanol, etc.), ethers, acetone, ethyl acetate, halogenated solvents (methylene chloride, chloroform, etc.), hexane and pentane. Additional solvents include water. When water is the complexing solvent, the complex is termed a "hydrate.”
  • subject or “patient” refer to a mammal, preferably a human, in need of treatment for a condition, such as cancer, disorder, or disease.
  • TAF refers to a TBP-associated factor .
  • the TAF is a TAF H , i.e., a TAF protein involved in mediating transcriptional activation of a eukaryotic gene transcribed by RNA polymerase II.
  • a TAF protein interacts with other transcriptional activators or repressors (Goodrich and Tjian, Curr Opin Cell Biol 6(3):4O3-9 (1994); Albright and Tjian, Gene 242(1 -2):1-13 (2000)).
  • a TAF is preferably from human, mouse,
  • TAF protein interacting with a GLI is a TAF H 31 protein.
  • Klemm et al. cloned a human TFIID subunit, which they termed hTAFn32 (Klemm et al.
  • TAF ⁇ 32 was functional in a partial recombinant TFnD complex and that the recombinant complex mediated activation by a GAL4-VP16 fusion protein.
  • TAF H 32 and TAFii31 are two names for the same protein, which is nowadays also referred to as TAF9.
  • TAF9 encodes a 264-amino acid protein. Immune-precipitation and binding analyses showed interaction of TAF9 with the N- terminal domain of p53 at sites identical to those bound by MDM2, the major cellular negative regulator of p53 activity.
  • the terms "treat”, “treating”, and “treatment” include: (1) preventing a disease, such as cancer, i.e. causing the clinical symptoms of the disease not to develop in a subject that may be predisposed to the disease but does not yet experience any symptoms of the disease; (2) inhibiting the disease, i.e. arresting or reducing the development of the disease or its clinical symptoms; or (3) relieving the disease, i.e.
  • Treatment means any manner in which the symptoms or pathology of a condition, disorder, or disease are ameliorated or otherwise beneficially altered.
  • the subject in need of such treatment is a mammal, more preferable a human.
  • Tumor cell refers to precancerous, cancerous, and normal cells in a tumor.
  • Wnt refer to a family of mammalian genes and encoded proteins related to the Drosophila segment polarity gene, wingless. In humans, the Wnt family of genes typically encode 38 to 43 IcDa cysteine rich glycoproteins having hydrophobic signal sequence, and a conserved asparagine-linked oligosaccharide consensus sequence (Shimizu et al. ⁇ Cell Growth Differ 8(12):1349-58 (1997)). The Wnt family contains at least 19 mammalian members.
  • Exemplary Wnt proteins include Wntl, Wnt2, Wnt3, Wnt3A, Wnt4, Wnt5A, Wnt5B, Wnt6, Wnt7A, Wnt7B, Wnt8A, Wnt8B, WNTlOA, WntlOB, Wntl 1, Wntl2, Wntl3, Wntl4, Wntl5, and Wntl6.
  • a preferred Wnt protein of the invention is Wnt2, preferably a human Wnt2 protein.
  • Transcriptional activation domains share little sequence homology and generally lack a folded structure in the absence of their target binding proteins.
  • GLI, GLI2, and GLI3 are believed to contact the TBP-associated factor, TAF H 31, through an ⁇ -helical domain found within their transcriptional activation domain (see Figure 3).
  • TAF H 31 TBP-associated factor
  • transcriptional activation domains are individually well conserved among different species, they are quite different among themselves.
  • the transactivation domains human GLIl, NH 2 -DSLDLDNTQLDFVAILDE-COOH (human GLIl, amino acid residues 1037- 1054), and mouse GLIl, NH 2 -DSLDLDNTQLDFVAILDE-COOH ( mouse GLIl, amino acid residues 1040- 1057) are identical.
  • the VP 16 activation domain undergoes an induced transition from a random coil to an ⁇ - helix upon binding to its target protein, TAF u31 and three residues believed to make direct contacts with TAFn31 have been identified: D472, F479, and L483(Uesugi et al, 1997, Science, 277:1310-1313) These three amino acid residues are also found within the activation domain of human GLIl (D1040, F1048, and L1052), which comprises the FXX ⁇ (FVAIL).
  • FXX ⁇ motifs have also been described within the activation domains of the tumor suppressor gene p53 and in NF-kB p65. MDM2, the cellular attenuator of p53, discriminates the FXX ⁇ motif of p53 of those of NF- k B p65 and VPl 6 and specifically inhibits p53 activity (Uesugi and Verdine, 1999, Proc. Natl. Acad. ScL USA, 96(26): 14801 -14806).
  • the activation domain of a polypeptide I comprising a FXX ⁇ motif can be differentiated from the activation domain of polypeptide II also comprising a FXX ⁇ motif, but having a different amino acid sequence.
  • a small molecule compound that significantly inhibits GLI3 signaling, but not significantly GLI or GLI2 signaling.
  • a small molecule compound is provided that differently affects the transcriptional activation potential of GLIl, GLI2, and GLI3.
  • a small molecule compound inhibits or reduces the binding of GLI3 to a TAF, preferably TAF ⁇ 31.
  • a small molecule compound that mimics an FXX ⁇ motif of a GLI protein, preferably a human or mouse GLI protein.
  • the small molecule compound mimics the FXX ⁇ motif ofGLD, FDAII (see Figure 3).
  • a small molecule compound mimics the FXX ⁇ motif of GLI2, FDAIM. In yet another embodiment of the present invention, the small compound molecule mimics the FXX ⁇ motif of GLIl, FVAIL.
  • the compounds of the present invention include small molecule compounds of the formula
  • each of X 1 and X 2 is independently N or C 5 wherein one of X 1 and X 2 is N and one of X 1 and X 2 is C, such that the ring N forms a double bond with whichever of X 1 and X 2 is C.
  • each of R 1 , R 2 and R 3 is independently selected from the group consisting of Ci-Ce alkyl, aryl, heteroaryl, cycloalkyl and heterocycloalkyl, optionally substituted with 0-3 R 6 groups each independently selected from the group consisting of H, halogen, Ci-Ce alkyl, -OR 7 , -C(O)R 7 , -OC(O)R 7 , -N(R 7 , R 7 ), -NR 7 S(O) 2 R 7 , -C(O)N(R 7 , R 7 ), -N(R 7 )C(O)R 7 , -N(R 7 )C(O)N(R 7 , R 7 ), -C(NR 7 )N(R 7 , R 7 ), -N(R 7 )C(NR 7 )N(R 7 , R 7 ) and S(O) 1n R 7 wherein subscript m is 0, 1 or 2.
  • Y is a direct bond or Cj-C 4 alkyl
  • Z is a member selected from the group consisting OfCi-C 4 alkyl, aryl and heteroaryl.
  • R 4 is H, halogen, -OR 7 , -OC(O)R 7 , -C(O)OR 7 , -N(R 7 , R 7 ), -NR 7 S(O) 2 R 7 , -C(O)N(R 7 , R 7 ), -N(R 7 )C(O)N(R 7 , R 7 ), -C(NR 7 )N(R 7 , R 7 ) and S(O) m R 7 wherein subscript m is 0, 1 or 2.
  • R 5 is H, Ci-C 6 alkyl, or optionally combined with Y to form a 5 to 6 membered heterocycle.
  • Each R 7 is independently H or Ci- C 6 alkyl.
  • the present invention provides a small molecule compound of the formula where each of R 1 , R 2 and R 3 is aryl. In a further embodiment, each of R 1 , R 2 and R 3 is phenyl.
  • the present invention provides a small molecule compound of the formula where R 4 is hydroxy.
  • Z is C 1 -C4 alkyl.
  • Z is aryl.
  • Z is phenyl.
  • the present invention provides a small molecule compound of the formula where each of R 1 , R 2 and R 3 is phenyl, where Y is C1-C4 alkyl, where Z is CV C 4 alkyl or phenyl, and where R 4 is hydroxy.
  • preferred small molecule compounds of the present invention include, but are not limited to, the following:
  • the small molecule compounds of the present invention can be prepared via condensation of ethyl cinnamate and benzaldehyde phenylhydrazone, followed by saponification of the ethyl ester and reaction with an amine to afford the desired amide end- product ⁇ see Example 3).
  • the small molecule compounds of the present invention can be prepared by first reacting cinnamic acid with the amine to prepare the amide, then condensation with the benzaldehyde phenylhydrazone.
  • One of skill in the art will recognize that additional methods exist for the preparation of the small molecule compounds of the present invention.
  • a small molecule compound of the present invention comprises a label. This is particular useful for detecting and testing the distribution of the small molecule compound after administration in vivo.
  • 3H can be used as a label in conventional pharmacokinetic/dynamic studies.
  • a small molecule compound comprising a label can be detected by, for example, spectroscopic, photochemical, biochemical, immunochemical, chemical, or other physical means.
  • a small molecule compound of the present invention may also contain unnatural proportions of atomic isotopes at one or more of the atoms that constitute such compounds.
  • the compounds may be radiolabeled with radioactive isotopes, such as for example tritium ( 3 H) or carbon-14 ( 14 C). All isotopic variations of the compounds of the present invention, whether radioactive or not, are intended to be encompassed within the scope of the present invention.
  • radioactive isotopes such as for example tritium ( 3 H) or carbon-14 ( 14 C). All isotopic variations of the compounds of the present invention, whether radioactive or not, are intended to be encompassed within the scope of the present invention.
  • a small molecule compound of the present invention can be screened for activity in vitro and in vivo.
  • this invention provides cell-based cytotoxicity assays, and apoptosis assays as described herein (e.g., see Example 1).
  • this invention provides mouse xenograft assays as described herein (e.g., see Examples 33-35 ).
  • the present invention provides a pharmaceutical composition or a medicament comprising at least one small molecule compound of the present invention and optionally a pharmaceutically acceptable carrier.
  • a pharmaceutical composition or medicament can be administered to a patient for the treatment of, for example, a condition, such as cancer.
  • compositions or medicaments for use in the present invention can be formulated by standard techniques using one or more physiologically acceptable carriers or excipients. Suitable pharmaceutical carriers are described herein and in "Remington's Pharmaceutical Sciences” by E.W. Martin.
  • the small molecule compounds of the present invention and their physiologically acceptable salts and solvates can be formulated for administration by any suitable route, including via inhalation, topically, nasally, orally, parenterally, or rectally.
  • the administration of the pharmaceutical composition may be made by intradermal, subdermal, intravenous, intramuscular, intranasal, intracerebral, intratracheal, intraarterial, intraperitoneal, intravesical, intrapleural, intracoronary or intratumoral injection, with a syringe or other devices.
  • Transdermal administration is also contemplated, as are inhalation or aerosol administration. Tablets and capsules can be administered orally, rectally or vaginally.
  • a pharmaceutical composition or a medicament can take the form of, for example, a tablets or a capsule prepared by conventional means with a
  • tablets and gelatin capsules comprising the active ingredient, i.e., a small molecule compound of the present invention, together with (a) diluents or fillers, e.g., lactose, dextrose, sucrose, mannitol, sorbitol, cellulose (e.g., ethyl cellulose, micro crystalline cellulose), glycine, pectin, polyacrylates and/or calcium hydrogen phosphate, calcium sulfate, ; (b) lubricants, e.g., silica, talcum, stearic acid, its magnesium or calcium salt, metallic stearates, colloidal silicon dioxide, hydrogenated vegetable oil, corn starch, sodium benzoate, sodium acetate and/or polyethyleneglycol; for tablets also (c) binders, e.g., magnesium aluminum silicate, starch paste, gelatin, tragacanth, methylcellulose, sodium carboxymethylcellulose,
  • Tablets may be either film coated or enteric coated according to methods known in the art.
  • Liquid preparations for oral administration can take the form of, for example, solutions, syrups, or suspensions, or they can be presented as a dry product for constitution with water or other suitable vehicle before use.
  • Such liquid preparations can be prepared by conventional means with pharmaceutically acceptable additives, for example, suspending agents, for example, sorbitol syrup, cellulose derivatives, or hydrogenated edible fats;
  • emulsifying agents for example, lecithin or acacia
  • non-aqueous vehicles for example, almond oil, oily esters, ethyl alcohol, or fractionated vegetable oils
  • preservatives for example, methyl or propyl-p-hydroxybenzoates or sorbic acid.
  • the preparations can also contain buffer salts, flavoring, coloring, and/or sweetening agents as appropriate. If desired, preparations for oral administration can be suitably formulated to give controlled release of the active compound.
  • the compounds may be conveniently delivered in the form of an aerosol spray presentation from pressurized packs or a nebulizer, with the use of a suitable propellant, for example, dichlorodifluoromethane, trichlorofluoromethane, dichlorotetrafluoroethane, carbon dioxide, or other suitable gas.
  • a suitable propellant for example, dichlorodifluoromethane, trichlorofluoromethane, dichlorotetrafluoroethane, carbon dioxide, or other suitable gas.
  • the dosage unit can be determined by providing a valve to deliver a metered amount.
  • Capsules and cartridges of, for example, gelatin for use in an inhaler or insufflator can be formulated containing a powder mix of the compound and a suitable powder base, for example, lactose or starch.
  • the small molecule compounds of the present invention can be formulated for parenteral administration by injection, for example by bolus injection or continuous infusion.
  • Formulations for injection can be presented in unit dosage form, for example, in ampoules or in multi-dose containers, with an added preservative.
  • Injectable compositions are preferably aqueous isotonic solutions or suspensions, and suppositories are preferably prepared from fatty emulsions or suspensions.
  • the compositions maybe sterilized and/or contain adjuvants, such as preserving, stabilizing, wetting or emulsifying agents, solution promoters, salts for regulating the osmotic pressure and/or buffers.
  • the active ingredient can be in powder form for constitution with a suitable vehicle, for example, sterile pyrogen-free water, before use. Ih addition, they may also contain other therapeutically valuable substances.
  • a suitable vehicle for example, sterile pyrogen-free water
  • the compositions are prepared according to conventional mixing, granulating or coating methods, respectively, and contain about 0.1 to 75%, preferably about 1 to 50%, of the active ingredient.
  • Suitable formulations for transdermal application include an effective amount of a compound of the present invention with carrier.
  • Preferred carriers include absorbable pharmacologically acceptable solvents to assist passage through the skin of the host.
  • transdermal devices are in the form of a bandage comprising a backing member, a reservoir containing the compound optionally with carriers, optionally a rate controlling barrier to deliver the compound to the skin of the host at a controlled and predetermined rate over a prolonged period of time, and means to secure the device to the skin.
  • Matrix transdermal formulations may also be used.
  • Suitable formulations for topical application are preferably aqueous solutions, ointments, creams or gels well-known in the art. Such may contain solubilizers, stabilizers, tonicity enhancing agents, buffers and preservatives.
  • the compounds can also be formulated in rectal compositions, for example, suppositories or retention enemas, for example, containing conventional suppository bases, for example, cocoa butter or other glycerides.
  • the compounds can be formulated as a depot preparation. Such long- acting formulations can be administered by implantation (for example, subciitaneously or intramuscularly) or by intramuscular injection.
  • the compounds can be formulated with suitable polymeric or hydrophobic materials (for example as an emulsion in an acceptable oil) or ion exchange resins, or as sparingly soluble derivatives, for example, as a sparingly soluble salt.
  • suitable polymeric or hydrophobic materials for example as an emulsion in an acceptable oil
  • ion exchange resins for example as sparingly soluble derivatives, for example, as a sparingly soluble salt.
  • the compositions can, if desired, be presented in a pack or dispenser device that can contain one or more unit dosage forms containing the active ingredient.
  • the pack can, for example, comprise metal or plastic foil, for example, a blister pack;
  • the pack or dispenser device can be accompanied by instructions for administration.
  • a pharmaceutical composition or medicament comprises an effective amount of a compound of the present invention as defined above, and another therapeutic agent, such as a chemotherapeutic agent.
  • chemotherapeutic agents include, but are not limited to, daunorubicin, daunomycin, dactinomycin, doxorubicin, epirubicin, idarubicin, esorubicin, bleomycin, mafosfamide, ifosfamide, cytosine arabinoside, bis-chloroethylnitrosurea, busulfan, mitomycin C, actinomycin D, mithramycin, prednisone, hydroxyprogesterone, testosterone, tamoxifen, dacarbazine, procarbazine, hexamethylmelamine, pentamethylmelamine, mitoxantrone, amsacrine, chlorambucil, methylcyclohexylnitrosurea,
  • chemotherapeutic agent may be used individually (e.g., 5-FU and small molecule compound), sequentially (e.g., 5-FU and small molecule compound for a period of time followed by e.g., MTX and small molecule compound), or in combination with one or more other such chemotherapeutic agents (e.g., 5-FU, MTX and small molecule compound, or 5-FU, radiotherapy and small molecule compound).
  • Administration may be by the same or different route of administration or together in the same pharmaceutical formulation.
  • a therapeutically effective amount of a small molecule compound of the present invention is administered in combination with surgery, and optionally administration of another chemotherapeutic agent.
  • a pharmaceutical composition or medicament is administered to a patient at a therapeutically effective dose to prevent, treat, or control cancer.
  • the pharmaceutical composition or medicament is administered to a patient in an amount sufficient to elicit an effective therapeutic response in the patient.
  • An effective therapeutic response is a response that at least partially arrests or slows the symptoms or complications of the disease. An amount adequate to accomplish this is defined as
  • the dosage of active small molecule compound administered is dependent on the species of warm-blooded animal (mammal), the body weight, age, individual condition, surface area of the area to be treated and on the form of administration.
  • the size of the dose also will be determined by the existence, nature, and extent of any adverse effects that accompany the administration of a particular small molecule compound in a particular subject.
  • a unit dosage for oral administration to a mammal of about 50 to 70 kg may contain between about 5 and 500 mg of the active ingredient.
  • a dosage of the active small molecule compound of the present invention is a dosage that is sufficient to achieve the desired effect.
  • Optimal dosing schedules can be calculated from measurements of small molecule compound accumulation in the body of a subject. In general, dosage is from 1 ng to 1,000 mg per kg of body weight and may be given once or more daily, weekly, monthly, or yearly. Persons of ordinary skill in the art can easily determine optimum dosages, dosing
  • a pharmaceutical composition or medicament comprising a small molecule compound of the present invention is administered in a daily dose in the range from about 1 mg of small molecule compound per kg of subject weight (1 mg/kg) to about lg/kg for multiple days.
  • the daily dose is a dose in the range of about 5 mg/kg to about 500 mg/kg.
  • the daily dose is about 10 mg/kg to about 250 mg/kg.
  • the daily dose is about 25 mg/kg to about 150 mg/kg.
  • the daily dose can be administered once per day or divided into subdoses and administered in multiple doses, e.g., twice, three times, or four times per day.
  • a small molecule compound must be administered for multiple days at the therapeutically effective daily dose.
  • therapeutically effective administration of a small molecule compound to treat cancer in a subject requires periodic (e.g., daily) administration that continues for a period ranging from three days to two weeks or longer.
  • a small molecule compound will be administered for at least three consecutive days, often for at least five consecutive days, more often for at least ten, and sometimes for 20, 30, 40 or more consecutive days. While consecutive daily doses are a preferred route to achieve a therapeutically effective dose, a therapeutically beneficial effect can be achieved even if the small molecule compound is not administered daily, so long as the administration is repeated frequently enough to maintain a therapeutically effective concentration of the small molecule compound in the subject.
  • a dosing schedule for example, is described in Examples 33-35 and in Figures 15-17.
  • Optimum dosages, toxicity, and therapeutic efficacy of such small molecule compounds may vary depending on the relative potency of individual small molecule compounds and can be determined by standard pharmaceutical procedures in cell cultures or experimental animals, for example, by determining the LD5 0 (the dose lethal to 50% of the population) and the ED 50 (the dose therapeutically effective in 50% of the population).
  • the dose ratio between toxic and therapeutic effects is the therapeutic index and can be expressed as the ratio, LD50/ED50.
  • Compounds that exhibit large therapeutic indices are preferred. While compounds that exhibit toxic side effects can be used, care should be taken to design a delivery system that targets such compounds to the site of affected tissue to minimize potential damage to normal cells and, thereby, reduce side effects.
  • the data obtained from, for example, cell culture assays and animal studies can be used to formulate a dosage range for use in humans.
  • the dosage of such small molecule compounds lies preferably within a range of circulating concentrations that include the ED 50 with little or no toxicity.
  • the dosage can vary within this range depending upon the dosage form employed and the route of administration.
  • the therapeutically effective dose can be estimated initially from cell culture assays.
  • a dose can be formulated in animal models to achieve a circulating plasma concentration range that includes the IC50 (the concentration of the test compound that achieves a half-maximal inhibition of symptoms) as determined in cell culture.
  • IC50 the concentration of the test compound that achieves a half-maximal inhibition of symptoms
  • levels in plasma can be measured, for example, by high performance liquid chromatography (HPLC).
  • HPLC high performance liquid chromatography
  • the dose equivalent of a small molecule compound is from about 1 ng/kg to 100 mg/kg for a typical subject.
  • the method of detecting a cancer comprises determining the level of a GLI polypeptide, preferably a GLIl, GLI2, or GLI3 polypeptide in a biological sample from a subject, such as a patient.
  • the level of an activator fragment of a GLI3 protein comprising a transcription activation domain is determined. Detecting an increase in the level of the GLI polypeptide, preferably the GLIl, GLI2, or GLI3 polypeptide or an increase in the level of an activator fragment of the GLI3 protein relative to normal indicates the presence of cancer in the subject.
  • Upregulation of, for example, GLIl, GLI2, or GLI3 expression is indicative of and can be correlated with various cancers.
  • a GLIl, GLI2, or GLI3 polypeptide or a GHl, Gli2, or GH3 polynucleotide can be used as a biomarker in the diagnosis of cancer.
  • the amount of a GLI protein, e.g., a GLI3, in a biological sample is determined.
  • the amount of GLI3 in a biological sample provided from a normal, healthy or non-cancer subject is correlated with the amount of GLB in a biological sample provided from a cancer subject or from a subject suspected of having cancer.
  • the amount of GLI3 detected in the biological sample from the cancer subject or from the subject suspected of having cancer may be specific for a given cancer.
  • Detection of, for example, a GLI polypeptide, such as a GLI3 polypeptide can be accomplished by any specific detection method including, but not limited to, affinity capture, mass spectrometry, traditional immunoassay directed to GLI3, PAGE, Western Blotting, or HPLC as further described herein or as known by one skilled in the art.
  • Detection paradigms that can be employed to this end include optical methods, electrochemical methods (voltametry and amperometry techniques), atomic force
  • radio frequency methods e.g., multipolar resonance spectroscopy.
  • optical methods in addition to microscopy, both confocal and non-confbcal, are detection of fluorescence, luminescence, chemiluminescence, absorbance, reflectance, transmittance, and birefringence or refractive index (e.g., surface plasmon resonance, ellipsometry, a resonant mirror method, a grating coupler waveguide method or
  • the method of detecting cancer comprises determining the level of a transcript encoding a GLI polypeptide, preferably a GLI3 polypeptide (see e.g., Genbank accession NM 007191 and SEQ ID NO: 1) in a biological sample from a subject, such as a patient. Detecting an increase in the level of the GIi mRNA, preferably the GLI3 mRNA relative to normal indicates the presence of cancer in the subject.
  • the step of determining the level of the GH mRNA comprises an amplification reaction.
  • the presence of cancer is evaluated by determining in a cell the level of expression of mRNA encoding a GLI polypeptide.
  • a GIi mRNA level higher than in a corresponding non-cancerous tissue indicates the presence of cancer.
  • Methods of evaluating RNA expression of a particular gene are well known to those of skill in the art, and include, inter alia, hybridization and amplification based assays. 1. Direct Hybridization-based Assays
  • Methods of detecting and/or quantifying the level of GH gene transcripts (mRNA or cDNA made therefrom) using nucleic acid hybridization techniques are known to those of skill in the art.
  • one method for evaluating the presence, absence, or quantity of GU polynucleotides, e.g., GH3 polynucleotides involves a Northern blot.
  • Gene expression levels can also be analyzed by techniques known in the art, e.g., dot blotting, in situ hybridization, RNase protection, probing DNA microchip arrays, and the like.
  • amplification-based assays are used to measure the expression level of a GIi gene, preferably the Gli3 gene, hi such an assay, the GIi nucleic acid sequences act as a template in an amplification reaction (e.g., Polymerase Chain
  • PCR PCR Reaction, or PCR
  • the amount of amplification product will be proportional to the amount of template in the original sample. Comparison to appropriate controls provides a measure of the level of GIi mRNA in the sample.
  • Methods of quantitative amplification are well known to those of skill in the art. Detailed protocols for quantitative PCR are provided, e.g., in Innis et al. (1990) PCR Protocols, A Guide to Methods and Applications, Academic Press, Inc. N.Y.).
  • the known nucleic acid sequences for GIi is sufficient to enable one of skill to routinely select primers to amplify any portion of the gene.
  • a semi-quantitative RT-PCR analysis is described, e.g., in Example 1 and in Figure 2.
  • a TaqMan based assay is used to quantify the cancer-associated polynucleotides.
  • TaqMan based assays use a fluorogenic oligonucleotide probe that contains a 5' fluorescent dye and a 3' quenching agent. The probe hybridizes to a PCR product, but cannot itself be extended due to a blocking agent at the 3' end.
  • the 5' nuclease activity of the polymerase e.g., AmpliTaq, results in the cleavage of the TaqMan probe.
  • This cleavage separates the 5' fluorescent dye and the 3' quenching agent, thereby resulting in an increase in fluorescence as a function of amplification (see, for example, literature provided by Perkin-Elmer, e.g., www2.perkin- elmer.com).
  • LCR ligase chain reaction
  • LCR ligase chain reaction
  • transcription amplification Kwoh et ai., Proc. Natl. Acad. ScL USA 86:1173(1989)
  • self-sustained sequence replication Guatelli et al, Proc. Nat. Acad. ScL USA 87: 1874(1990)
  • dot PCR and linker adapter PCR, etc.
  • the small molecule compounds of the present invention find use in a variety of ways.
  • the present invention provides methods for using the small molecule compounds of the present invention to, for example, (i) induce apoptosis in a cell expressing a GLI polypeptide, (ii) inhibit unwanted growth, proliferation or survival of a cell expressing a GLI polypeptide, (iii) treat a condition, such as a cancer, expressing a GLI polypeptide, (iv) inhibit expression of a gene having a GLI DNA binding site, and (v) inhibit the activity of a GLI polypeptide.
  • Any cell or tumor cell expressing a GLI polypeptide, preferably a GLI3 polypeptide can be used to practice a method of the present invention.
  • a preferred cell or tumor cell expressing a GLI polypeptide is selected from the group consisting of colon cancer, melanoma, mesothelioma, lung cancer, renal cell carcinoma, breast cancer, prostate cancer, sarcoma, ovarian cancer, esophageal cancer, gastric cancer, hepatocellular cancer,
  • nasopharyngeal cancer pancreatic cancer
  • glioma cell nasopharyngeal cancer, pancreatic cancer, and glioma cell.
  • Methods of the present invention can be practiced in vitro or in vivo.
  • Apoptosis plays a central role in both the development and homeostasis of multicellular organisms.
  • "Apoptosis” refers.to programmed cell death and is characterized by certain cellular characteristics, such as membrane blobbing, chromatin condensation and fragmentation, formation of apoptotic bodies and a [positive "TUNEL" (terminal
  • deoxynucleotidyl transferase-mediated UTP nick end-labeling staining pattern.
  • a later step in apoptotic process is the degradation of the plasma membrane, rendering apoptotic cells leaky to various dyes (e.g., propidium iodide).
  • Apoptosis can be induced by multiple independent signaling pathways that converge upon a final effector mechanism consisting of multiple interactions between several death receptors and their ligands, which belong to the tumor necrosis factor (TNF)
  • TNF tumor necrosis factor
  • the best-characterized death receptors are CD95 ("Fas"),
  • TNFRl p55
  • death receptor 3 DR3 or Apo3/TRAMO
  • DR4 and DR5 apo2-TRAIL-R2
  • the final effector mechanism of apoptosis is the activation of a series of proteinases designated as caspases. The activation of these caspases results in the cleavage of a series of vital cellular proteins and cell death.
  • the present invention provides methods for inducing apoptosis in a cell expressing a GLI protein.
  • the method for inducing apoptosis in a cell comprises the step of exposing the cell to a composition or contacting the cell with a composition comprising a small molecule compound of the present invention.
  • the composition comprises small molecule compound FNl -5.
  • the composition comprises small molecule compound FN1-8.
  • the cells are exposed to or contacted with an effective amount of the composition wherein the contacting results in inducing apoptosis.
  • the GLI protein is GLI2 or GLI3.
  • exposing a cell to a composition comprising a small molecule of the invention comprises introducing the composition into the cell.
  • a method of inducing a tumor cell to undergo apoptosis comprising the step of administering a small molecule compound of the present invention.
  • the small molecule compound is FN 1-5.
  • the small molecule compound is FNl -8.
  • the cells are exposed ex vivo to or contacted ex vivo with the composition.
  • the cell is exposed in vivo to or contacted in vivo with the composition.
  • a method for inhibiting at least one of unwanted growth, hyperproliferation, or survival of a cell comprises the step of determining whether the cell expresses a GIi gene or alternatively a GLI polypeptide. This method also comprises the step of contacting the cell with an effective amount of a small molecule of the present invention, wherein the step of contacting results in the inhibition of at least one of unwanted growth, hyperproliferation, or survival of the cell.
  • hyperproliferation, or survival of a cell is inhibited is selected from the group consisting of colon cancer cell, melanoma cell, mesothelioma cell, lung cancer cell, renal cell carcinoma cell, breast cancer cell, prostate cancer cell, sarcoma cell, ovarian cancer cell, esophageal cancer cell, gastric cancer cell, hepatocellular cancer cell, nasopharyngeal cancer cell, pancreatic cancer cell, and glioma cell.
  • GLI polypeptide preferably a GLI3
  • Proliferation refers to the growth of a cell, the reproduction or multiplication of a cell or morbid cysts.
  • This method comprises the step of contacting the cell with an amount of a small molecule compound effective to inhibit proliferation of the cell.
  • a small molecule compound effective to inhibit proliferation of the cell.
  • small molecule compounds FN1-5 or FN1-8 either alone or in combination are useful for inhibiting proliferation of a cell, preferably a cancer cell.
  • this method is practiced in vitro. As further described herein, methods of the present invention can also be practiced in vivo.
  • the small molecule compounds of the present invention are used to prevent the formation of a metastasis.
  • This method comprises the step of administering to a tumor cell a small molecule compound of the present invention wherein the administering results in prevention from metastasis.
  • the small molecule compound is FN 1-5.
  • the small molecule compound is FNl -8.
  • the cell expressing a GLI protein and being contacted with a small molecule compound of the present invention is a cancer cell selected from the group consisting of colon cancer, melanoma, mesothelioma, lung cancer, renal cell carcinoma, breast cancer, prostate cancer, sarcoma, ovarian cancer, esophageal cancer, gastric cancer, hepatocellular cancer, nasopharyngeal cancer, pancreatic cancer, and glioma cell.
  • a preferred cancer cell is a lung cancer cell, a colon cancer cell, or a melanoma cell.
  • a method for treating a subject suffering from a cancerous condition comprises the step of administering to the subject a therapeutically effective amount of a small molecule compound, wherein the cancerous condition is characterized by expressing a GLI polypeptide, preferably a GLIl, GLI2, or GLB polypeptide, and wherein the step of administering results in the treatment of the subject.
  • a GLI polypeptide preferably a GLIl, GLI2, or GLB polypeptide
  • a preferred cancerous condition or cancer is selected from the group consisting of colon cancer, melanoma, mesothelioma, lung cancer, renal cell carcinoma, breast cancer, prostate cancer, sarcoma, ovarian cancer, esophageal cancer, gastric cancer, hepatocellular cancer,
  • nasopharyngeal cancer pancreatic cancer
  • glioma nasopharyngeal cancer, pancreatic cancer, and glioma.
  • a small molecule compound is used to treat a subject suffering from a colon cancer expressing a GLI polypeptide, preferably a GLIl, GLI2, or GLB polypeptide.
  • a small molecule compound is used to treat a subject suffering from a breast cancer expressing a GLI polypeptide, preferably a GLIl, GLI2, or GLB polypeptide.
  • a small molecule compound is used to treat a subject suffering from a nasopharyngeal cancer expressing a GLI polypeptide, preferably a GLIl , GLI2, or GLB polypeptide.
  • a small molecule compound is used to treat a subject suffering from a lung cancer expressing a GLI polypeptide, preferably a GLIl, GLI2, or GLB polypeptide.
  • a lung cancer includes, but is not limited to, bronchogenic carcinoma [squamous cell, undifferentiated small cell, undifferentiated large cell,
  • adenocarcinoma alveolar [bronchiolar] carcinoma, bronchial adenoma, sarcoma, lymphoma, chondromatous hamartoma, mesothelioma, SCLC, and NSCLC.
  • a small molecule compound is used to treat a subject suffering from a sarcoma expressing a GLI polypeptide, preferably a GLIl , GLI2, or GLB polypeptide.
  • a sarcoma includes, but is not limited to, cancers such as angiosarcoma, fibrosarcoma, rhabdomyosarcoma, liposarcoma, myxoma, rhabdomyoma, fibroma, lipoma and teratoma.
  • a small molecule compound is used to treat a subject suffering from a gastrointestinal cancer expressing a GLI polypeptide, preferably a GLIl, GLI2, or GLI3 polypeptide.
  • a gastrointestinal cancer includes, but is not limited to cancers of esophagus [squamous cell carcinoma, adenocarcinoma,
  • leiomyosarcoma lymphoma] stomach [carcinoma, lymphoma, leiomyosarcoma], pancreas [ductal adenocarcinoma, insulinoma, glucagonoma, gastrinoma, carcinoid tumors, VIPoma], small bowel [adenocarcinoma, lymphoma, carcinoid tumors, Kaposi's sarcoma, leiomyoma, hemangioma, lipoma, neurofibroma, fibroma], and large bowel [adenocarcinoma, tubular adenoma, villous adenoma, hamartoma, leiomyoma].
  • a small molecule compound is used to treat a subject suffering from a cancer of the genitourinary tract expressing a GLI
  • cancers of the genitourinary tract include, but are not limited to cancers of kidney [adenocarcinoma, Wilms tumor (nephroblastoma), lymphoma, leukemia, renal cell carcinoma], bladder and urethra
  • adenocarcinoma, sarcoma [adenocarcinoma, sarcoma], and testis [seminoma, teratoma, embryonal carcinoma, teratocarcinoma, choriocarcinoma, sarcoma, Leydig cell tumor, fibroma, fibroadenoma, adenomatoid tumors, lipoma],
  • a small molecule compound is used to treat a subject suffering from a liver cancer expressing a GLI polypeptide, preferably a GLIl, GLI2, or GLD polypeptide.
  • a liver cancer includes, but is not limited to,
  • hepatocellular carcinoma cholangiocarcinoma, hepatoblastoma, angiosarcoma,
  • hepatocellular adenoma hepatocellular adenoma
  • hemangioma hepatocellular adenoma
  • a small molecule compound is used to treat a subject suffering from a skin cancer expressing a GLI polypeptide, preferably a GLIl, GLI2, or GLI3 polypeptide.
  • Skin cancer includes, but is not limited to, malignant melanoma, basal cell carcinoma, squamous cell carcinoma, Kaposi's sarcoma, nevi, dysplastic nevi, lipoma, angioma, dermatofibroma, keloids, and psoriasis.
  • a small molecule compound is used to treat a subject suffering from a gynecological cancer expressing a GLI polypeptide, preferably a GLIl, GLI2, or GLI3 polypeptide.
  • Gynecological cancers include, but are not limited to, cancer of uterus [endometrial carcinoma], cervix [cervical carcinoma, pre-invasive cervical dysplasia], ovaries [ovarian carcinoma (serous cystadenocarcinoma, mucinous cystadenocarcinoma, endometrioid carcinoma, clear cell adenocarcinoma, unclassified carcinoma), granulosa-theca cell tumors, Sertoli-Leydig cell tumors, dysgerminoma, malignant teratoma and other germ cell tumors], vulva [squamous cell carcinoma, intraepithelial carcinoma, adenocarcinoma, fibrosarcoma, melanoma], vagina [clear cell carcinoma, squamous cell carcinoma, sarcoma botryoides (embryonal rhabdomyosarcoma), and fallopian tubes [carcinoma].
  • endometrial carcinoma endometrial carcinoma
  • a small molecule compound is used to treat a subject suffering from a bone cancer expressing a GLI polypeptide, preferably a GLIl, GLI2, or GLI3 polypeptide.
  • Bone cancer includes, but is not limited to, osteogenic sarcoma [osteosarcoma], fibrosarcoma, malignant fibrous histiocytoma, chondrosarcoma, Ewing's sarcoma, malignant lymphoma [reticulum cell sarcoma], multiple myeloma, malignant giant cell tumor, chordoma, osteochondroma [osteocartilaginous exostoses], benign chondroma, chondroblastoma, chondromyxoid fibroma, osteoid osteoma, and giant cell tumors.
  • a small molecule compound is used to treat a subject suffering from a cancer of the nervous system expressing a GLI polypeptide, preferably a GLIl, GLI2, or GLD polypeptide.
  • Cancers of the nervous system include, but are not limited to cancers of skull [osteoma, hemangioma, granuloma, xanthoma, Paget's disease of bone], meninges [meningioma, meningiosarcoma, gliomatosis], brain
  • astrocytoma medulloblastoma, glioma, ependymoma, germinoma (pinealoma), glioblastoma multiforme, oligodendroglioma, schwannoma, retinoblastoma, congenital tumors]
  • spinal cord neurofibroma, meningioma, glioma, sarcoma.
  • a small molecule compound is used to treat a subject suffering from a hematologic cancer expressing a GLI polypeptide, preferably a GLIl, GLI2, or GLB polypeptide.
  • Hematologic cancers include, but are not limited to cancer of blood [myeloid leukemia (acute and chronic), acute lymphoblastic leukemia, chronic lymphocytic leukemia, myeloproliferative diseases, multiple myeloma,
  • a small molecule compound is used to treat a subject suffering from a cancer of adrenal glands expressing a GLI polypeptide, preferably a GLIl, GLI2, or GLI3 polypeptide.
  • a cancer of adrenal glands includes, but is not limited to, neuroblastoma.
  • the present invention provides a method for treatment or prevention of a cancer wherein a GLI polypeptide, preferably a GLIl, GLI2, or GLI3 polypeptide is expressed.
  • this method comprises the step of administering to a patient a pharmaceutical composition.
  • Such pharmaceutical composition comprises, for example, a small molecule compound of the present invention.
  • the small molecule compound is FN 1-5.
  • the small molecule compound is FNl -8.
  • Pharmaceutical compositions of the present invention are administered alone or in combination with one or more additional therapeutic compound or treatments. Examples of such therapeutic compounds or treatments include, but are not limited to, taxol, cyclophosphamide, tamoxifen, fluoruracil and doxorubicin.
  • other chemotherapeutic agents are described herein.
  • Methods for treating cancer may optionally comprise one or more of the following steps: obtaining a biological sample of tissue or fluid from an individual; screening the biological sample for the expression of a GLI polypeptide, preferably a GLIl, GLI2, or GLB polypeptide, for example by contacting the biological sample with an antibody directed to GLIl, GLI2, or GLI3; or screening the biological sample for expression of a GUI, Gli2, or Gli3 polynucleotide, for example by detecting a GUI , GH2, or Gli3 mRNA.
  • a GLI polypeptide preferably a GLIl, GLI2, or GLB polypeptide
  • a small molecule compound of the present invention is used to overcome resistance to chemotherapeutic agents in tumor cells.
  • This method comprises the step of administering to a tumor cell resistant to at least one chemotherapeutic agent a small molecule compound of the present invention, wherein the administering results in subsequent tumor cell death.
  • the small molecule compound is FNl -5.
  • the small molecule compound is FNl -8.
  • GLI polypeptide such as a GLIl , GLI2, or GLI3 polypeptide
  • GLI functions as a transcriptional activator
  • inhibition of GLI transcriptional activity by the methods of the present invention should also inhibit or down-regulate the expression of down-stream genes i.e., genes whose expression is regulated by GLI, preferably by GLIl , GLI2, or GLI3.
  • GLI typically regulates expression of down-stream genes by binding to its cognate DNA binding site operably linked to the promoter and/or enhancer sequence of down-stream genes.
  • a DNA binding site for GLD has been described (Vortkamp et al. 1995, DNA Cell. Biol 14:629-34; Hallikas et al, 2006, Cell 124(l):47-59).
  • a GLIl, GLI2, or GLI3 down-stream gene is identified.
  • identification of a GLIl, GLI2, or GLI3 down-stream gene is performed by DNA sequencing of the promoter and/or enhancer region of a gene suspected to be regulated by GLIl, GLI2, or GLI3. It is expected that a GLIl, GLI2, or GLI3 down-stream gene is also expressed or over-expressed in cancers wherein GLIl, GLI2, or GLI3 is expressed or over-expressed.
  • GLI down-stream genes having a GLI DNA binding site can also be identified by fragmenting a genome and use the resulting fragments as probes in gel shift assay as known in the art.
  • Any fragment identified in such an assay can be amplified, identified and/or used as a nucleic acid probe to screen for and identify the gene from where it originated, by e.g., screening a genomic DNA library as known in the art.
  • An alternative method for identifying GLI binding sites in mammalian enhancer elements and, thus, GLI target genes is the enhancer element locator (EEL; Hallikas et al., 2006, Cell 124:47-59). For example, Hallikas et al. identified several enhancer elements with two or more GLI binding sites that are conserved in mouse to human and rat to human alignments.
  • GLI target genes such as exocyst complex component Sec5 (SEC5L1), NULL (NM_018271; NM_144962), early growth response protein 3 (EGR-3) (zinc finger protein pilot) (EGR3), PR-domain zinc finger protein 10 (PRDMlO), T-box transcription factor TBX2 (T-box protein 2; TBX2), SOX-13 protein (type 1 diabetes autoantigen ICA 12) (islet cell antigen 12) (SOXl 3), patched protein homolog 1 (PTCl) (PTC) (PTCH), and protein related to DAN and Cerberus (NM_022469).
  • EGR-3 zinc finger protein pilot
  • PRDMlO PR-domain zinc finger protein 10
  • T-box transcription factor TBX2 T-box protein 2; TBX2
  • SOX-13 protein type 1 diabetes autoantigen ICA 12
  • SOXl 3 patched protein homolog 1
  • PTCl PTC
  • PTCH protein related to DAN and Cerberus
  • a GLI down-stream gene having a GLI DNA binding site, preferably a GLIl , GLI2, or GLI3 DNA binding site, operably linked to its promoter and/or enhancer sequence is inhibited.
  • Inhibition of the down-stream gene is achieved by using a method of the present invention for inhibiting GLI signaling.
  • this invention provides a method for inhibiting the expression of a GLI3 down- stream gene, comprising the step of administering to a cell expressing a GLI3 down-stream gene a small molecule compound of the present invention, wherein said administering results in inhibition of expression of the GLD down-stream gene.
  • this method includes the step of verifying inhibition of the GLI3 down-stream gene. This can be done using methods in the art, such as RT-PCR or Western blot analysis.
  • the down-stream gene is a Wnt gene, preferably a Wnt-2 gene and more preferably a human Wnt2 gene.
  • inhibition of GLI3 signaling leads to inhibition or down-regulation of Wnt-2 as well as the Wnt-2 signaling. Inhibition of Wnt-2 signaling affects, for example expression of DvI and beta-catenin as described in U.S. Patent
  • GLI3 functions upstream of GLIl and GLI2 and also seems to regulate transcription of the GUI and Gli2 genes through binding to a GLI3 DNA binding site within the promoter/enhancer regions of the GIi 1 and Gli2 genes.
  • signaling by GLI3, GLIl and GLI2 is not in parallel, but rather within the same signaling pathway.
  • the down-stream gene is a GIi 1 gene, preferably a human GIi 1 gene.
  • inhibition of GLI3 signaling leads to inhibition or down-regulation of GUI expression as well as the GLIl signaling.
  • the down-stream gene is a GH2 gene, preferably a human Gli2 gene.
  • inhibition of GLI3 signaling leads to inhibition or down-regulation of Gli2 expression as well as the GLI2 signaling.
  • GLI polypeptides have several biological activities as described herein.
  • a method for inhibiting the activity of a GLI polypeptide preferably a GLIl, GLI2, or GLI3 polypeptide. This method comprises the step of contacting a GLI polypeptide with a small molecule compound of the invention thereby inhibiting the activity of the GLI polypeptide.
  • this method comprises the step of contacting a cell expressing a GLI polypeptide with a small molecule compound of the invention thereby inhibiting the activity of the GLI polypeptide.
  • GLI polypeptides are transcriptional activator proteins and typically exert their transcriptional activation potential through binding to or interaction with a TBP- Associated Factor (TAF).
  • TAF TBP- Associated Factor
  • a method for inhibiting the activity of a GLI polypeptide comprises the step of contacting a GLI polypeptide with a small molecule compound of the invention thereby inhibiting binding of the GLI polypeptide to a TAF or interaction of the GLI polypeptide with a TAF.
  • this method comprises the step of contacting a cell expressing a GLI polypeptide with a small molecule compound of the invention thereby inhibiting binding of the GLI polypeptide to a TAF or interaction of the GLI polypeptide with a TAF.
  • GLI polypeptides are transcriptional activator proteins and typically exert some of their transcriptional activation potential through binding to or interaction with a co-activator, such as CBP.
  • a method for inhibiting the activity of a GLI polypeptide comprises the step of contacting a GLI polypeptide with a small molecule compound of the invention whereby the binding of the GLI polypeptide to a co-activator or interaction of the GLI polypeptide with a co-activator is inhibited.
  • this method comprises the step of contacting a cell expressing a GLI polypeptide with a small molecule compound of the invention thereby inhibiting binding of the GLI polypeptide to a co- activator or interaction of the GLI polypeptide with a co-activator.
  • GLI polypeptides are transcriptional activator proteins. and typically exert their transcriptional activation potential through binding to a GLI DNA binding site.
  • a method for inhibiting the activity of a GLI polypeptide comprises the step of contacting a GLI polypeptide with a small molecule compound of the invention thereby inhibiting binding of the GLI polypeptide to a GLI DNA binding site.
  • this method comprises the step of contacting a cell expressing a GLI polypeptide with a small molecule compound of the invention thereby inhibiting binding of the GLI polypeptide to a GLI DNA binding site.
  • Inhibition of the activity of the GLI polypeptide can be in vitro or in vivo.
  • Another aspect of the invention provides for the use of a small molecule compound of the present invention in the manufacture of a pharmaceutical composition or a medicament for the therapeutic and/or prophylactic treatment of a condition, e.g., cancer wherein a GLI polypeptide, preferably a GLI3 polypeptide, is expressed.
  • a condition e.g., cancer wherein a GLI polypeptide, preferably a GLI3 polypeptide, is expressed.
  • the present invention provides for the use of a small molecule compound in the manufacture of a pharmaceutical composition or medicament for inducing apoptosis in a cancer cell, wherein the cancer cell expresses a GLI polypeptide, preferably a GLI3 polypeptide.
  • the invention provides for the use of a small molecule compound in the manufacture of a pharmaceutical composition or medicament for use in combination with another chemotherapeutic anticancer agents for the treatment of a cancer expressing a GLI polypeptide, preferentially a GLI3 polypeptide.
  • compositions and medicaments provided by the present invention are described herein.
  • modulators of GLI protein activity are identified using methods known in the art and described herein. A number of different screening protocols can be utilized to identify additional compounds than those described herein that modulate the activity of a GLI polypeptide.
  • modulate encompasses an increase or a decrease in the measured activity of a GLI polypeptide when compared to a suitable control.
  • screening protocols can be used in cells, particularly mammalian cells, and especially human cells. And even more preferred in human cancer cells.
  • the screening methods involve screening a variety of compounds to identify a compound that modulates activity of a GLI polypeptide.
  • the method generally comprises the step of (a) contacting a candidate compound with a GLI polypeptide, with a sample comprising a GLI polypeptide or a mammalian cell expressing a GLI polypeptide; and (b) assaying an activity of the GLI polypeptide in the presence of the candidate compound.
  • An increase or a decrease in the activity measured in comparison to the activity of the GLI polypeptide in a suitable control is an indication that the candidate compound modulates an activity of the GLI polypeptide.
  • Compounds that increase or decrease a GLI polypeptide activity to a desired extent may be selected for further study, and assessed for cellular availability, pharmacokinetic analysis, cytotoxicity, biocompatibility, etc.
  • the screening methods involve screening candidate
  • the screening methods involve screening candidate compounds to identify a compound that increase the activity of a GLI polypeptide.
  • the present invention provides a method for identifying a compound that modulates a GLI protein activity.
  • a preferred method of this invention is a method for identifying a candidate compound capable of modulating the protein-protein interaction between a GLI protein and a TAF ⁇ 31 protein.
  • this method comprises the steps of contacting a candidate compound with a sample comprising a GLI protein and a TAF II 31 protein; and determining the binding of the GLI-protein to the TAF ⁇ 31 protein.
  • a reduced binding of the GLI protein to the TAFn31 in the presence of the candidate compound compared to the binding of the GLI protein to the TAF H 31 in the absence of the candidate compound indicates that the candidate compound is capable of inhibiting the interaction between the GLI protein and the TAFn31 protein.
  • An increased binding of the GLI protein to the TAFii31 in the presence of the candidate compound compared to the binding of the GLI protein to the TAF ⁇ 31 in the absence of the candidate compound indicates that the candidate compound is capable of increasing the interaction between the GLI protein and the TAF ⁇ 31 protein.
  • the GLI protein activity is GLI protein dependent transcription activity and the method is for identifying a compound that modulates GLI protein dependent transcription activity.
  • the method comprises the steps of contacting a sample with a candidate compound, wherein the sample comprises an expression reporter construct having one or more GLI DNA binding sites operably linked to a reporter gene; and determining the effect, if any, of the candidate compound on the level of GLI protein dependent transcription activity.
  • reporter genes as known in the art may be used. Suitable reporter genes include, but are not limited to luciferase, CAT (chlorarnphenicol-acetyltransferase) , GFP (green fluorescent protein), and ⁇ -Gal (beta-galactosidase).
  • the binding assays described herein such as immunoprecipitation assays and transcription assays (see, e.g., Examples 35)
  • the modulation of binding of a GLI polypeptide to a TAF H 31 protein in the absence or presence of an candidate compound can be assessed.
  • assays described herein can be employed in screening protocols wherein the small molecule compounds analyzed in these assays are replaced by candidate compounds to be tested.
  • a method for identifying a candidate compound for inducing apoptosis comprises the steps of (a) contacting a GLI polypeptide with a candidate compound, and (b) determining whether the candidate compound binds to the GLI polypeptide, inhibits an activity of the GLI polypeptide; wherein a candidate compound that binds to the GLI polypeptide or inhibits an activity of the GLI polypeptide is a candidate compound useful for inducing apoptosis.
  • the methods for identifying a candidate compound as described herein comprise the step of selecting the compound that binds to a GLI polypeptide or modulates the activity of the GLI polypeptide.
  • Candidate compounds useful for inducing apoptosis identified by the method described herein can be assessed by using the apoptosis assay described herein and assays known in the art.
  • a candidate compound is assessed for any cytotoxic activity it may exhibit towards normal cells (e.g., non-cancer cells), using well-known assays, such as trypan blue dye exclusion, an MTT ([3-(4,5-dimethylthiazol-2-yl)-2,5-d- iphenyl-2H-tetrazolium bromide]) assay, and the like. Compounds that do not exhibit cytotoxic activity are considered candidate compounds.
  • a two-hybrid system utilizing cells may be used ("MATCHMAKER Two-Hybrid system”, “Mammalian MATCHMAKER Two-Hybrid Assay Kit”, “MATCHMAKER one-Hybrid system”
  • a GLI polypeptide is fused to an SRF- binding region or GAL4-binding region and expressed in yeast cells.
  • a TAF ⁇ 31 polypeptide that binds to the GLI polypeptide is fused to the VP 16 or GAL4 transcriptional activation region and also expressed in the yeast cells.
  • the TAF ⁇ 31 polypeptide that binds to the GLI polypeptide may be fused to the SRF-binding region or GAL4-binding region, and the GLI polypeptide to the VP 16 or GAL4 transcriptional activation region.
  • the binding of the two activates a reporter gene, making positive clones detectable.
  • a reporter gene for example, Ade2 gene, lacZ gene, CAT gene, luciferase gene and such can be used besides HIS3 gene.
  • the non-binding of the two polypeptides is also detectable (e.g., no expression of the lazZ gene results in white yeast colonies, while expression of the lacZ gene results in blue colonies).
  • test compound for example, cell extracts, cell culture supernatant, products of fermenting microorganism, extracts from marine organism, plant extracts, purified or crude proteins, peptides, non-peptide compounds, synthetic micromolecular compounds and natural compounds can be used in the screening methods of the present invention.
  • the test compound of the present invention can be also obtained using any of the numerous approaches in combinatorial library methods known in the art, including (1) biological libraries, (2) spatially addressable parallel solid phase or solution phase libraries, (3) synthetic library methods requiring deconvolution, (4) the "one-bead one-compound” library method and (5) synthetic library methods using affinity chromatography selection.
  • test compound exposed to a cell or protein according to the screening methods of the present invention may be a single compound or a combination of compounds. When a combination of compounds is used in the screening methods of the invention, the compounds may be contacted sequentially or simultaneously.
  • a compound isolated by the screening methods of the present invention is a candidate for drugs which modulate the activity of a GLI polypeptide, for inducing apoptosis, and for treating or preventing a pathological condition, such as cancer, as described herein.
  • Methods for testing and assaying compounds, agents, or antagonists identified by methods described herein, involve a variety of accepted tests to determine whether a given compound, agent, or small molecule compound is useful to practice a method of the present invention.
  • Methods of the present invention may optionally comprise the step of detecting a nucleic acid, such as a mRNA (e.g., by nucleic acid hybridization or PCR), a polypeptide (e.g., by Western blotting, immunological assay, or mass spectrometry), an enzymatic activity (e.g., enzymatic activity of a reporter gene product, such as luciferase), or inducing or inhibiting apoptosis. These detection methods are well known in the art. VI. KITS
  • kits are also provided by the invention.
  • such kits may include any or all of the following: assay reagents, buffers, a small molecule compound of the present invention, a GLI polypeptide, a GIi nucleic acid, an anti-GLI antibody, hybridization probes and/or primers, GIi expression constructs, etc.
  • a therapeutic product may include sterile saline or another pharmaceutically acceptable emulsion and suspension base.
  • kits may include instructional materials containing directions (i.e., protocols) for the practice of the methods of this invention.
  • the instructions may be present in the subject kits in a variety of forms, one or more of which may be present in the kit.
  • instructional materials typically comprise written or printed materials they are not limited to such. Any medium capable of storing such instructions and communicating them to an end user is contemplated by this invention. Such media include, but are not limited to electronic storage media ⁇ e.g., magnetic discs, tapes, cartridges, chips), optical media (e.g., CD ROM), and the like. Such media may include addresses to internet sites that provide such instructional materials.
  • kits and components can be prepared according to the present invention, depending upon the intended user of the kit and the particular needs of the user.
  • the kit is a pharmaceutical kit and comprises a pharmaceutical composition comprising (i) a small molecule compound, preferably FN 1-5 or FNl -8 and (ii) a pharmaceutical acceptable carrier.
  • Pharmaceutical kits optionally comprise an instruction stating that the pharmaceutical composition can or should be used for treating a cancer expressing a GLI polypeptide or GIi nucleic acid, preferably a GLI3 polypeptide or Gli3 nucleic acid.
  • kits according to the present invention may further comprise a reagent for performing mass spectrometry.
  • reagents are well known to those skilled in the art and include, for example, a probe or a chip.
  • kits embodiments of the present invention include optional functional components that would allow one of ordinary skill in the art to perform any of the method variations described herein.
  • NSCLC NSCLC cells A549, H1703, H460, H358, H322, H838, H1299, H1650, H1975, and A427; mesothelioma cells 21 IH, H513, H2052, H28, and Met5A; colon cancer cells SW480, HCTl 16, HT29, Lovo, and CaCO2; breast cancer cells MCF7, HuLlOO, SKBR-3 and
  • BT474 sarcoma MG-63, MNNG, A-204, and SJSA-I
  • human normal skin fibroblast cell Malme-3
  • renal cell carcinoma cells 786-O, Caki, 769-P, A704, and OMRC3 prostate cancer cell line LnCAP; glioma cell line U87; hepatocellular carcinoma cells HepG2 and SK-Hep-1; normal muscle cell lines; normal renal cell line HRE 152 and HK-2.
  • Normal mesothelial cell line LP-9 was obtained from the Cell Culture Core Facility at Harvard University (Boston, Massachusetts).
  • Human pancreatic cancer cell lines BxPC3, Panc4.21, CFPAC-I, and L3.6sl were kindly provided by Dr. Matthias Hebrok's laboratory at the University of California, San Francisco (San Francisco, California).
  • Human nasopharyngeal carcinoma cell lines HNE-I and HONE-I were kindly provided by Dr.
  • SAEC normal human small airway epithelial cells
  • NHBE bronchial epithelial cells
  • Fresh cancer tissue and adjacent normal tissue from patients undergoing curative primary resection of their tumors were collected at the time of surgery (IRB approval H8714- 15319-040), and immediately snap-frozen in liquid nitrogen. These tissue samples were kept at -170 0 C in a liquid nitrogen freezer until further use.
  • Primary tissue cultures were prepared as follows: Fresh cancer tissue was obtained with consent from patients undergoing resection, cut into small pieces (1-2 mm in diameter), and then digested with Collagenase A (Roche Applied Science, Indianapolis, Indiana) at room temperature for 2 hours according to manufacture's protocol.
  • the small molecule compounds of the present invention were dissolved in DMSO at a concentration of 30 mM.
  • the small molecule compounds were then tested under cell culture conditions at different concentrations ranging from 0, 10, 30, 50, to 100 uM.
  • the cells were incubated with the small molecule compounds in 6-well plates for about 3 days. After removal of the cell culture medium, 1-ml of 0.5% crystal violet solution (prepared in 20% ethanol and 20% methanol) was added to stain the cells for 5 min. Then the crystal violet solution was rinsed clean with tap water. Cell survival was estimated based on the density of crystal stained plates.
  • MTS assay Another assay for determining the number of viable cells in proliferation or cytotoxicity assays is the MTS assay, a colorimetric method.
  • MTS assay reagents are commercially available (Promega Corp., Madison, Wisconsin).
  • the reagent contains a tetrazolium compound [3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4- sulfophenyl)-2H-tetrazolium, inner salt; MTS] and an electron coupling reagent (phenazine ethosulfate; PES).
  • PES has enhanced chemical stability, which allows it to be combined with MTS to form a stable solution.
  • the MTS tetrazolium compound (Owen.s reagent) is bioreduced by cells into a colored formazan product that is soluble in tissue culture medium. This conversion may be accomplished by NADPH or NADH produced by dehydrogenase enzymes in metabolically active cells.
  • the quantity of formazan product as measured by the absorbance at 490nm is directly proportional to the number of living cells in culture. Because the MTS formazan product is soluble in tissue culture medium, this assay requires fewer steps than procedures that use tetrazolium compounds such as MTT.
  • the formazan product of MTT reduction is a crystalline precipitate that requires an additional step in the procedure to dissolve the crystals before recording absorbance readings at 570nm.
  • Apoptosis was analyzed by using an Annexin V FITC Apoptosis Detection Kit (Biosource, Camarillo. CA), according to the manufacturer's protocol. After treatment with different small molecule compounds at various concentrations for about 3 days, cells were harvested by trypsinization, stained and immediately analyzed by flow cytometry (FACScan; Decton Dickinson, Franklin Lake, New Jersey). Early apoptotic cells with exposed phosphatidylserine but intact cell membranes will bind to Annexin V-FITC, but not propidium iodide (PI). Cells in necrotic or late apoptotic stages will be labeled with both Annexin V-FITC and PI. "% apoptotic cells” or "% apoptosis” refers to the combined early and late apoptotic cells.
  • RNA from cell lines or tissue samples was isolated using Qiagen RNeasy Mini Kit (Valencia, California).
  • RT-PCR was performed in GeneAmp PCR system 2700 (Applied Biosystems, Foster City, California) using One-step RT-PCR Kit from Invitrogen Life Technologies (Carlsbad, California).
  • Primers for RT-PCR were obtained from Operon Technologies Inc. (Alameda, California).
  • Primer sequences for amplifying different genes in Hedgehog and Wnt signaling pathways are listed in the table below (Table 1; F, forward primer; R, reverse primer). The expected size of the PCR product is indicated for each primer pair.
  • GAPDH was used as internal control.
  • TAF ⁇ 31 cDNA was kindly provided by Dr. Gregory L. Verdine at Harvard University (Cambridge, Massachusetts).
  • pTOPFLASH:pFOPFLASH luciferase activity each was normalized to luciferase activities of the pRL-TK reporter (co-transfected internal control). All experiments were performed in triplicate, and repeated three times.
  • Horseradish peroxidase-conjugated goat anti- rabbit or donkey anti-mouse antibodies were used as secondary antibodies. Proteins were visualized with chemihiminescence luminol reagents (Santa Cruz Bio-technology). Anti- Dvl-3, and anti-Survivin, antibodies were from Santa Cruz Biotechnology (Santa Cruz, California). Anti-Caspase3 antibody was from Oncogene (Cambridge, Massachusetts). Anti- ⁇ -Actin antibody was from Sigma- Aldrich Corp. (St. Louis, Missouri). Anti- ⁇ -catenin antibody was from Transduction Laboratories (Lexington, Kentucky). Anti-Cytochrome c antibody was from BD Biosciences (San Diego, California). For detecting alteration of ⁇ - catenin cytosolic extracts were prepared and examined as described previously in the publications from our lab.
  • mice Female athymic nude mice strain NCRNU-M (5- 10 weeks old, 20-25 grams in weight; Taconic, Germantown, New York) was maintained in pathogen-free conditions.
  • Ten mice were used in each group and injected s.c. with 3x10 6 cancer cells in the dorsal area in a volume of 100 ⁇ l.
  • mice After inoculation, human cancer cells were allowed to grow in mice for 7 days to become visible tumor nodules. Animals were then injected with small molecule compound FN1-8 at a dose of 50 mg/kg body weight (1 mg/mouse per day). DMSO alone was used as control. The compounds and controls were adjusted in 40 ul volume for i.p. injection in the abdomens of the mice. One mouse was sacrificed within 1 hour after the compound injection (after 6 injections) and its blood was collected. Then mass spectrometry was used to analyze the compound level in the blood sample to confirm the compound absorption into the blood stream of the mice. Injections were performed daily around the same time for 14 days. Tumors were allowed to grow for 1- 2 additional weeks after completion of the compound treatments. Tumor size was measured every three days, and tumor volumes were calculated using width (x) and length (y) (x 2 y/2, where x ⁇ y). Data was presented as mean values (+ S. D.).
  • tumors were resected from the mice of different treated groups after sacrificed. Resected tumors were cryo-dissected immediately and the tumor mass of each sample were then measured. TUNEL staining of the tumor specimens was performed using the ApopTag Peroxidase hi Situ Oligo Ligation Apoptosis Detection Kit (Chemicon International, Temecula, California) according to the
  • mice were resected from mice. These organs included liver, lung, heart, kidney, intestines, ovary, brain, spleen, skin, and muscle.
  • the specimens were fixed in 4% buffered formaldehyde, embedded in paraffin, sectioned, and histologically analyzed by hematoxylin and eosin (HE) staining.
  • HE stained slides were examined by a mouse pathologist for toxicity evidence from all the organs as compared with DMSO controls.
  • FN 1-3 was prepared by a similar manner to that of FN 1-5 by using n-butylamine instead of 4-(hydroxyphenyl)ethylamine. MS: 420.9 (M+Na), 398.9 (M+H), 325.5, 297.5.
  • FN1-7 was prepared by a similar manner to FNl -5 by using 3-aminopro ⁇ anol instead of 4-(hydroxyphe ⁇ yl)ethylamine. MS: 422.9 (M+Na), 400.9 (M+H), 325.5, 297.5.
  • dimehylformamide (2 mL) was kept at the room temperature for 1 hour.
  • the reaction mixture was diluted with ethyl acetate (20 mL), washed with water twice (10 mL each) followed by brine (10 mL), dried (Na 2 SO 4 ), and evaporated to isolate (4-methoxycarbonyl)butyl cinnamamide (1, 100 mg).
  • a mixture of (4-methoxycarbonyl)butyl cinnamamide (1, 100 mg), benzaldehyde phenylhydrazone (2, 113 mg), chloramine-T trihydrate (160 mg), and methanol (2 mL) were heated under refluxing for 22 hours.
  • the reaction mixture was diluted with 50% ethyl acetate in n-hexanes (40 mL), filtered, and evaporated.
  • the residue was purified by column chromatography (silica gel 20 g, eluent: 0 to 10% ethyl acetate gradient in hexanes) to isolate methyl 5-(l,3,5-triphenyl-4,5-dihydro-pyrazole-4- carbonyl)aminopentanoate (3, 13 mg) and methyl 5-(l,3,4-triphenyl-4,5-dihydro-pyrazole-5- carbonyl)aminopentanoate (4, 103 mg).
  • ESI-MS of FN1-9U (upper right panel) and FN1-9S (upper left panel).
  • FN1-9U shows bigger peaks at m/z- 297 than that of FN1-9S, because of the decarbonylated fragment formation (bottom panel).
  • FN2-1 Preparation of ethyl l,3-diphenyl-5-isobutyl-4,5-dihydro- pyrazole-4-carboxylate (FN2-1)
  • FN2-1 was prepared by a similar manner to FNl-I by using the ethyl 5-methyl-hex-2-enoate instead of the ethyl cinnamate in Example 2.
  • FN2-5 was prepared by a similar manner to FNl -5 by using FN2-1 instead of FNl- 1.
  • Ethyl l-phenyl-3 ) 5-bis(isobutyl)-4,5-dihydropyrazole-4-carboxylate was prepared by a similar manner to Example 2 by using ethyl 5-methyl-2-hexanoate instead of the ethyl cinnamate, and using 3-methylbutanal phenylhydrazone instead of the benzaldehyde phenylhydrazone, respectively, in Example 2.
  • FN3-5 was prepared by a similar manner to Example 4 by using the ethyl l-phenyl-3,5-bis(isobutyl)-4,5-dihydropyrazoIe-4-carboxylate instead of FNl-I in Example 4.
  • FIG. 2 An exemplary analysis of an RT- PCR detecting Gli3 expression is shown in Figure 2.
  • Figure 6 shows the result of a cytotoxicity assay testing small molecule compounds FN1-7, FNl -8, and FN3-5 on three NSCLC cell lines (H 1299, A549, and H460) and one colon cancer cell line (SW480). Cancer cell lines were plated in 6- well plates as described, and incubated with 50, and 100 ⁇ M of each compound (stocks were dissolved in DMSO at 30 mM) for 3 days. Dramatic cell killing was observed in all cancer cell lines tested for FNl -8, a modified version of small molecule compound FN 1-5. Apoptosis analysis was also carried out by using flow cytometry and the results were consistent (data not shown). Therefore, using the rational design design-screen approach described herein, additional small molecule compound, FN 1-8, inhibiting GLI3 transcription activation domain (TAF-binding domain) was identified.
  • TAF-binding domain GLI3 transcription activation domain
  • FNl -5 and FNl -8 in the cell-based cytotoxicity assay, a dramatic cell killing was observed in the human colon cancer cell lines LoVo and CaCO2 (data not shown). FN 1-8 seemed to more potent than FN 1-5 in cell killing. Both, small molecule compounds FNl -5 and FN 1-8 induced apoptosis in CaCO2 (Tables 2 and 3).
  • Example 7 Small Molecules FN1-5 But Not FN1-8 Induces Cell Killing And
  • Flow cytometry was used to examine apoptosis in colon cancer cell line HT29 after treatment of cells with small molecule compounds FN1-5 and FN1-8. While FN1-5 induced apoptosis in HT29 cells (at 50 ⁇ M 35% apoptotic cells were observed; Table 2), no apoptosis was observed after treatment with FNl -8 (Table 3). These results were consistent with the staining result above. Thus, the fact that small molecule compound FNl -8 does not affect survival and does not induce apoptosis in HT29 cells also confirms that the effects mediated by FNl -8 in other cell lines tested are not due to a general toxicity of FNl -8.
  • Example 8 Small Molecule Compounds FN1-5 And FN1-8 Induce Apoptosis
  • Flow cytometry was also used to examine apoptosis in several NSCLC cell lines after treatment with small molecule compounds of the invention. For example, after treatment with 100 ⁇ M FN 1-5 for 3 days, significant apoptosis was observed in the NSCLC cell lines H1299 (55.9% apoptosis), A549 (30.0% apoptosis) (see Table 2 for additional data). These results were consistent with the staining result.
  • FN I -5 and FN 1-8 in the cell-based cytotoxicity assay, a dramatic cell killing was observed in the NSCLC cell lines H460, H838, H1975, H1650, and H1703. Comparing same concentrations, FN1-8 seemed more potent than FN 1-5 in these cell lines (data not shown).
  • Small molecule compound FN 1-8 also significantly inhibited cell proliferation in NSCLC cells, including A549, H358, and H322 cells. This was shown by incubating the cells with either 7.5 ⁇ M or 15 ⁇ M of FN 1-8 and then performing a MTS assay according to the manufacturer's protocol at different time points after addition of the compound. It was found that FN 1-8 inhibited cell proliferation in these cells in a dose-dependent manner already after 1 day. (data not shown).
  • Example 9 Small Molecule Compounds FN1-5 And FN1-8 Induce Cell Killing
  • Flow cytometry was also used to examine apoptosis induced by molecule compounds of the invention, in primary cultured NSCLC cells freshly made from tissue samples. For example, after treatment with 10, 30, and 50 ⁇ M FN1-8 or 30 and 50 ⁇ M FNl- 5 for 3 days, significant apoptosis was observed in primary cultured NSCLC cells (data not shown). For example, app. 60% apoptotic cells were observed at 50 ⁇ M FN1-8. These result were consistent with results obtained in the cell-based cytotoxicity assay using primary cultured NSCLC cells (data not shown) and compounds FN 1-5 and FNl -8. Again, FN 1-8 was found to be more potent than FN 1-5 at the same concentration.
  • Example 10 Small Molecule Compounds FN1-5 And FN 1-8 Induce Apoptosis
  • Small molecule compound FNl -8 also significantly inhibited cell proliferation in melanoma cells, including Malme-3M, A375, G361, SK-Mel-2, SK-Mel-5, and SK-Mel-28 cell lines. This was shown by incubating the cells with either 5 ⁇ M or 10 ⁇ M of FNl -8 and then performing a MTS assay according to the manufacturer's protocol at different time points after addition of the compound. In Malme-3M, G361, SK-Mel-2, and SK-Mewl-28 FN 1-8 inhibited cell proliferation in these cells at 10 ⁇ M after 1-2 days and in A375 and SK- Mel-5 cells already after 1 day. (data not shown).
  • Flow cytometry was used to examine apoptosis in the mesothelioma cell line 21 IH after treatment of cells with small molecule compounds FN1-5 and FN1-8. Significant apoptosis in the mesothelioma cell line 21 IH was observed after treatment for 3 days with either 30 ⁇ M FN1-5 (37.5%; Table 2) or 30 ⁇ M FNl -8 (30.7%; Table 3).
  • the mesothelioma cell line MS-I was also incubated with 10, 30, 50, and 100 ⁇ M of compounds FN 1-9U and FNl-9S. While some cell killing was observed using 100 ⁇ M FN1-9U, no cell killing effect or apoptosis was observed using FN1-9S (data not shown).
  • the cell-based cytotoxicity assay described herein was used to determine the effect of small molecule compounds FN 1-5 and FNl -8 on the human prostate cancer cell line LnCAP. Viability of LnCAP cells was analyzed after treatment with 30 and 50 ⁇ M FN1-5 and after treatment with 10, 30, and 50 ⁇ M FN1-8. A dramatic cell killing was observed at 50 ⁇ M FN1-8 (data not shown). A much lesser cell killing effect of FNl -5 was observed (data not shown).
  • Flow cytometry was also used to examine apoptosis induced by molecule compounds FNl-5 and FN1-8 in LnCAP cells. After treatment with 10, 30, and 50 ⁇ M FNl- 8 or 30 and 50 ⁇ M FN 1-5 for 3 days, significant apoptosis was observed in LnCAP cells (Tables 2 and 3). For example, app.42% apoptotic cells were observed at 50 ⁇ M FN1-8. These result were consistent with results obtained in the cell-based cytotoxicity assay as described above Again, FN1-8 was found to be more potent than FNl-5 at the same concentration.
  • the cell-based cytotoxicity assay described herein was used to determine the effect of small molecule compounds FNl-5 and FNl -8 on the human pancreatic cancer cell lines L3.6sl, Panc4.21, BxPC3, and CFPAC-I. Viability of these cells was analyzed after treatment with 10, 30 and 50 ⁇ M FNl-5 or FNl -8. A dramatic cell killing was observed at 50 ⁇ M FNl-5 or FN1-8 in all human pancreatic cancer cell lines analyzed (data not shown). However, cell killing mediated by FNl-5 in Panc4.21 was less when compared to its effect on the three other pancreatic cancer cell lines.
  • the cell-based cytotoxicity assay described herein was used to determine the effect of small molecule compounds FN 1 -5 and FNl -8 in the human breast cancer cell line MCF-7. Viability of MCF-7 cells was analyzed after treatment with 30 and 50 ⁇ M FNl -5 and after treatment with 10, 30, and 50 ⁇ M FNl -8. A dramatic cell killing was observed at 50 ⁇ M FN1-8 and 50 ⁇ M FN1-5 (data not shown). FN1-8 was more potent in this assay than FN1-5.
  • Example 15 Effects Of Small Molecule Compounds FN1-5 And FN1-8 On
  • the cell-based cytotoxicity assay described herein was used to determine the effect of small molecule compounds FNl -5 and FNl -8 in the human ovarian cancer cell line AZ23247. Viability of AZ23247 cells was analyzed after treatment with 10, 30 and 50 ⁇ M FN1-5 or FN1-8. A dramatic cell killing was observed with both compounds at 30 ⁇ M and 50 ⁇ M (data not shown).
  • the cell-based cytotoxicity assay described herein was used to determine the effect of small molecule compounds FNl -5 and FNl -8 in the human renal cell carcinoma cell lines 786-O, Caki, and OMRC3. Viability of these cells was analyzed after treatment with 10, 30 and 50 ⁇ M FNl -5 or FN 1-8. A dramatic cell killing in all human renal cell carcinoma cell lines analyzed was observed at 50 ⁇ M FN1-8 and 50 ⁇ M FN1-5 (data not shown). FN1-8 was more potent in this assay than FN1-5.
  • Example 17 Effects Of Small Molecule Compounds FN1-5 And FN1-8 On
  • the cell-based cytotoxicity assay described herein was used to determine the effect of small molecule compounds FN1-5 and FN1-8 in the human esophageal cancer cell lines SEG-I, TE-7, BIC-I, and OE21. Viability of these cells was analyzed after treatment with 10, 30 and 50 ⁇ M FN 1-5 or FNl -8. A dramatic cell killing in all human esophageal cells analyzed was observed at 50 ⁇ M FNl -8 and 50 ⁇ M FN 1-5 (data not shown). FN 1-8 was more potent in this assay than FN 1-5.
  • Hh signaling in the human esophageal cancer cell lines SEG-I , TE-7, BIC-I, and OE21 was examined by semi-quantitative RT-PCR. Activation of Hh pathways, including expression of Ptch 1, GIi 1 GH2, and GH3 was found in those cell lines (data not shown).
  • the cell-based cytotoxicity assay described herein was used to determine the effect of small molecule compounds FN 1-5 and FNl -8 in the human gastric cancer cell lines NUGC3, MNK28, and AGS. Viability of these cells was analyzed after treatment with 10, 30 and 50 ⁇ M FN 1-5 or FNl -8. A dramatic cell killing in all human gastric cells analyzed was observed at 50 ⁇ M FN 1-8 and 50 ⁇ M FN 1-5 (data not shown). FN 1-8 was more potent in this assay than FN 1-5.
  • the cell-based cytotoxicity assay described herein was used to determine the effect of small molecule compounds FNl -5 and FNl -8 in the human sarcoma cell lines MG63 and MNNG. Viability of these cells was analyzed after treatment with 10, 30 and 50 ⁇ M FN 1-5 or FN1-8. A dramatic cell killing in all sarcoma cells analyzed was observed at 50 ⁇ M FNl- 8 (data not shown). No significant cell killing by FN1-5 was observed in these sarcoma cell lines (data not shown).
  • the cell-based cytotoxicity assay described herein was used to determine the effect of small molecule compounds FN1-5 and FN1-8 in the human hepatocellular carcinoma cell lines HEPG2 and SK-Hep-1. Viability of these cells was analyzed after treatment with 10, 30 and 50 ⁇ M FN 1-5 or FNl -8. A dramatic cell killing in all human gastric cells analyzed was observed at 50 ⁇ M FN1-8 and 50 ⁇ M FN1-5 (data not shown). FN1-8 seemed to be more potent in this assay than FN 1-5.
  • Example 21 Effects Qf Small Molecule Compounds FN1-5 And FN 1-8 In
  • the cell-based cytotoxicity assay described herein was used to determine the effect of small molecule compounds FNl -5 and FNl -8 in the human nasopharyngeal cancer cell lines HNEl and HONEl . Viability of these cells was analyzed after treatment with 10, 30 and 50 ⁇ M FN1-5 or FNl-8. A dramatic cell killing in all human gastric cells analyzed was observed at 50 ⁇ M FNl-8 and 50 ⁇ M FN1-5 (data not shown). FNl-8 was more potent in this assay than FN 1-5.
  • Viability of U87 cells was analyzed after treatment with 30 and 50 ⁇ M FN 1-5 and 10, 30, and 50 ⁇ M FNl-8. A dramatic cell killing was observed at 50 ⁇ M FNl-8 and to a lesser extent with 50 ⁇ M FNl-5 (data not shown).
  • FNl-8, FN1-7, and FNl-5 The cell killing effect of small molecule compounds FNl-8, FN1-7, and FNl-5 at different doses was examined in normal human muscle cells.
  • FNl -7 which has similar structure as the other two compounds, but does not have much cytotoxicity in cancer cell lines tested was included as a negative control.
  • Normal muscle cells were plated in 6-well plates and incubated with 1 , 10, 30, and 50 ⁇ M of each compound for 3 days, in the same manner as described herein for similar other experiments. No noticeable cell killing effect was observed for all compounds at all doses, suggesting that both FNl -5 and FNl-8 are not toxic to normal muscle cells. Both FNl-5 and FNl-8 seem to be specific in killing cancer cells.
  • Example 25 Summary Of Apoptosis Inducing Effect Of Small Molecule FN 1-5
  • Example 26 Summary Of Apoptosis Inducing Effect Of Small Molecule FN 1-8
  • the compounds were tested for regulate the expression of GIi down-stream target genes.
  • Wnt signaling has been shown to be activated down-stream of GH activation, and Hh/Gli signaling has been shown to regulate the expression of Wnt genes.
  • the human Wnt2 promoter was cloned and found to contain putative GIi-DNA binding sites within its promoter region (data not shown).
  • the Wnt2 promoter-luciferase reporter activity was assayed after treating the NSCLC cell line A549 (expressing Wnt2) with several small molecule compounds of the invention.
  • Example 28 Small Molecule Compounds FN1-5 And FN1-8 Modulate The
  • H460 and A549 cells were incubated with 30 ⁇ M of each compound (FN1-5 or FN1-8) for 2 days before isolation of total RNA that was used for semi-quantitative RT-PCR analysis.
  • Key components and direct target genes of the Hh pathway e.g., Ptchl and GHl were found to be downregulated (data not shown).
  • GAPDH served as a control.
  • the small molecule compounds FN 1-5 and FN 1-8 could also modulate the hedgehog pathway in the melanoma cell line LOX, the colon cancer cell line SW480 and in primary cultured human mesothelioma cells freshly made from tissue (data not shown). Interestingly, no noticeable changes were observed in HT29 cells (data not shown).
  • TAF ⁇ 31 expression plasmid contained the full-length T AF ⁇ 31 cDNA generated by PCR cloned into the EcoRI (5') and BamHI (3') sites of a mammalian expression vector containing a c-Myc tag (pCDNA3.1(-)B.
  • the sequence of TAF ⁇ 31 corresponds to GenBank Accession No. U25112.
  • SOCS3 promoter- luciferase reporter activity was measured after the treatment of the NSCLC cell line A549 with small molecule compounds FNl -5, FNl -7, FNl -8, and FN 1 -9U. After treatment for 18- 24 hours at 30 ⁇ M, both FN1-5 and FN1-8 were found inactive in regulating the SOCS3 promoter activity, similar as other compounds that have shown no cell killing effect (e.g., FN1-7 and FN1-9U; Figure 11). This result indicates that both FN1-5 and FN1-8 are specific small molecule inhibitors for the inhibition of GLI transcription activity.
  • GLI3 seems to activate transcription of GUI and Gli2 genes.
  • inhibition of GLI3 activity by small molecule compounds of the invention should also inhibit signaling by GLIl and/or GLI2. If so, then transfecting a GLIl and/or GLI2 expression construct into a cell treated with a small molecule compound of the present invention, should lead to at least a partial rescue of the apoptotic effect mediated by the small molecule compound.
  • FNl -5 the specificity of the small molecule compound FNl -5, as well as its inhibitory mechanisms, it was tested whether over-expressing GLI2 protein could attenuate the cell killing effect of FN1-5.
  • the colon cancer cell line SW480 was transfected with either empty pCDNA3 vector or with a GH2 cDNA expression construct. After selection, the transfected cells were re-plated in 6-well plates at same numbers, and then FN 1-5 was added into medium at a final concentration of 50 ⁇ M. After 5 days, FN 1-5 was found to kill less cells transfected with GH2 than those with empty vector (data not shown). This result indicated that FNl -5 killed cancer cells by inhibiting the GLB transcription activator function. [0341] To further examine the specificity of the small molecule compound FN1-8, as well as its inhibitory mechanisms, we tested whether over-expressing GLI2 protein could attenuate the cell killing effect of FNl -8.
  • the transfection experiment was performed as described above. After 5 days, apoptosis analysis using flow cytometry was performed to quantify the experiment. Significantly more apoptotic cells were found in SW480 cells transfected with empty vector (48.1%) than in SW480 cells transfected with the GH2 expression construct
  • GLI/TAF II 31 induced 6xGLI BS-luciferase transcription was reduced.
  • transcription activity by GLI alone was reduced by approximately 30%
  • transcription activity in the A549 cells cotransfected with TAF K 31 was reduced by about 50% for GLI2 and by about 70% for GLIl .
  • FN1-8 may be a specific inhibitor of the interaction between GLI proteins and T AFn31.
  • GLIl-TAFbd (Nm)-LDSLDLDNTQLDFVAILDEPQG-(COOH); GLI2-TAFbd: (NH2)-VDSQLLEAPQIDFDAIMDDGDH-(COOH); and GlLI-TAFbd: (NH2)-LDSHDLEGVQIDFDAIIDDGDH-(COOH)
  • TAFii31 proteins were prepared by using the TNT quick coupled
  • GLI-peptide/TAF ⁇ 31 protein-protein interaction assay can also be used in a method for screening for agents that inhibit the protein-protein interaction assay between a GLI protein (or GLI peptide as described above). In this method, an agent to be validated or screened for would be incubated with a GLI protein (or GLI peptide) and a TAFH31 protein, as described above.
  • Example 36 Small Molecule Compound FN1-8 Suppresses Tumor Growth In
  • Tumor size (length and width according to their shapes) was measured with a caliper every three days. Tumor volumes were calculated using the equation x 2 y (where x ⁇ y). As can be seen in Figures 17 and 18, tumor growth was significantly suppressed after treatment with the small molecule compound FN 1-8.
  • FNl -8 Three weeks after the initial tumor inoculation and the treatment as described above, tumors were dissected from the mice of each group and their weights were measured using a scale. Tumor weight dramatically decreased after the treatment with FNl -8 compound ( Figures 18B and 18C).
  • Example 37 Small Molecule Compound FN1-8 Suppresses Tumor Growth In
  • Tumor size was measured with a caliper every three days. Tumor volumes were calculated using the equation x 2 y (where x ⁇ y). As can be seen in Figure 16A, tumor growth was not affected after treatment with the small molecule compound FNl -8. This result is consistent with in vitro data showing no effect of FN 1-8 on GLI3 activation in HT29 cells and no Gli3 RT-PCR product (e.g., see Figure 12 and data not shown). Tumor weight after the treatment with FN 1-8 is similar to the DMSO control group ( Figure 20B). Results are the means ⁇ SD (error bars).
  • the compounds and DMSO were adjusted in a volume of 50 ⁇ l for i.p. injection in the abdomens of the mice. 43 days after the initial tumor inoculation, tumors were dissected from the mice of each group and their weights were measured using a scale. It was found that HT29 tumor weight after the treatment with FN1-8 was similar to the DMSO control group (data not shown).
  • tumors were dissected from the mice of each group and their weights were measured using a scale. Tumor weight decreased after treatment with FN 1 -8 compound compared to the DMSO control group (data not shown). This low dose in vivo result is consistent with in vitro data presented herein.
  • FNl -5 concentration in each plasma sample was determined by mass spectroscopy and is shown in Fig.21 A. This analysis shows a quick uptake of FN1-5 into plasma within 10 min after the compound injection. The FNl -5 concentration in the serum then diminishes within 24 hours, suggesting that FNl -5 can be absorbed in vivo.

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Abstract

La présente invention concerne des compositions, des méthodes et des trousses pour diagnostiquer et traiter des cancers exprimant un polypeptide GLI, et en particulier un polypeptide GLI1, GLI2 ou GLI3. L'invention concerne des composés à petites molécules imitant le domaine d'activation transcriptionnelle d'un polypeptide GLI. Les inhibiteurs à petites molécules de l'invention bloquent spécifiquement la fonction activatrice d'un polypeptide GLI, mais pas la fonction répressive de GLI3.
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WO2013013190A1 (fr) 2011-07-21 2013-01-24 The Regents Of The University Of California Ciblage de protéines gli dans un cancer humain par des petites molécules
EP2547368A4 (fr) * 2010-03-19 2014-08-06 Univ South Alabama Méthodes et compositions pour le traitement du cancer
EP3144034A1 (fr) * 2008-11-12 2017-03-22 The Trustees of the University of Pennsylvania Agents de stimulation de la voie de signalisation de la protéine shh pour le traitement de la chute des cheveux
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US9840470B2 (en) 2013-01-23 2017-12-12 The Regents Of The University Of California Targeting GLI proteins in human cancer by small molecules

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